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Elnedyn and time step limit
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11 years 10 months ago #971
by josef
Elnedyn and time step limit was created by josef
Hello Martini developers,
I have some questions about running an MD simulation of a protein ELNEDYN model with ~ 200 residues solvated in a box of 8 nm size neutralized with 10 NA+. I have revised this and several gromacs forums, but it is not clear how to run MD with dt = 20 fs without the next warning and error:
WARNING 1 : The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option. Should I ignore this warning? The MD simulation eventually fails with LINCS warning: Step 81051, time 1621.02 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.143304, max 0.404759 (between atoms 13 and 15) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12 13 89.8 0.2193 0.2197 0.2200 14 12 89.9 0.2566 0.1768 0.2550 13 15 74.0 0.2485 0.3512 0.2500 15 14 58.9 0.2805 0.3427 0.2800 Step 81052, time 1621.04 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 202.120215, max 505.372597 (between atoms 14 and 12) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12 13 79.0 0.2197 70.6136 0.2200 14 12 90.8 0.1768 129.1250 0.2550 13 15 88.6 0.3512 74.7561 0.2500 15 14 90.2 0.3427 114.4250 0.2800 Wrote pdb files with previous and current coordinates Segmentation fault If I change dt = 10 or 15 fs, I am able to run without warnings or segmentation faults up to 300 ns so far even with the same warning: The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 p, which is less than the time step of 1.0e-02 ps. Some details are a bit confusing, is it correct to have backbone bonds with force constants of 150000 without being constrained? This is the default output of the Protein.itp file created by martinize-1.1.py and the value reported in Periole, 2009 ELNEDYN paper. Should I modify the masses of SC or BB beads? My protocol consists of: 1. I use martinize-1.1.py and the specified command options in the tutorial. 2. I do a minimization of the system with position restraints in all beads and stiff bonds for beads in the aromatic side-chains and VAL, MET, THR, SER and so on. (I also performed a short minimization in vacuum with the same conclusions). 3. I do a short equilibration 50 ps with position restraints in all beads and replace stiff bonds by constraints in aromatic beads and some other side-chains (t = 1 fs) 4. I perform 5 ns equilibration with position restraints in backbone beads and dt = 10fs. It fails with dt =20 fs 5. I perform production simulations with dt = 10 – 15 fs. It fails with dt = 20 fs. I am able to run MD using a similar protocol without problems for the same protein with dt = 30 fs without elastic network. Thank you in advance. Jose[file system.top, line 19]:
The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an
estimated oscillational period of 9.7e-02 ps, which is less than 5 times
the time step of 2.0e-02 ps.
Maybe you forgot to change the constraints mdp option.
Should I ignore this warning?
The MD simulation eventually fails with LINCS warning:
Step 81051, time 1621.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.143304, max 0.404759 (between atoms 13 and 15)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
12 13 89.8 0.2193 0.2197 0.2200
14 12 89.9 0.2566 0.1768 0.2550
13 15 74.0 0.2485 0.3512 0.2500
15 14 58.9 0.2805 0.3427 0.2800
Step 81052, time 1621.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 202.120215, max 505.372597 (between atoms 14 and 12)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
12 13 79.0 0.2197 70.6136 0.2200
14 12 90.8 0.1768 129.1250 0.2550
13 15 88.6 0.3512 74.7561 0.2500
15 14 90.2 0.3427 114.4250 0.2800
Wrote pdb files with previous and current coordinates
Segmentation fault
If I change dt = 10 or 15 fs, I am able to run without warnings or segmentation faults up to 300 ns so far even with the same warning:
The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 p, which is less than the time step of 1.0e-02 ps.
Some details are a bit confusing, is it correct to have backbone bonds with force constants of 150000 without being constrained? This is the default output of the Protein.itp file created by martinize-1.1.py and the value reported in Periole, 2009 ELNEDYN paper. Should I modify the masses of SC or BB beads?
My protocol consists of:
1. I use martinize-1.1.py and the specified command options in the tutorial.
2. I do a minimization of the system with position restraints in all
beads and stiff bonds for beads in the aromatic side-chains and VAL, MET, THR, SER and so on. (I also performed a short minimization in vacuum with the same conclusions).
3. I do a short equilibration 50 ps with position restraints in all beads and replace stiff bonds by constraints in aromatic beads and some other side-chains (t = 1 fs)
4. I perform 5 ns equilibration with position restraints in backbone beads and dt = 10fs. It fails with dt =20 fs
5. I perform production simulations with dt = 10 – 15 fs. It fails with dt = 20 fs.
I am able to run MD using a similar protocol without problems for the same protein with dt = 30 fs without elastic network.
Thank you in advance.
Jose
I have some questions about running an MD simulation of a protein ELNEDYN model with ~ 200 residues solvated in a box of 8 nm size neutralized with 10 NA+. I have revised this and several gromacs forums, but it is not clear how to run MD with dt = 20 fs without the next warning and error:
WARNING 1 : The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option. Should I ignore this warning? The MD simulation eventually fails with LINCS warning: Step 81051, time 1621.02 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.143304, max 0.404759 (between atoms 13 and 15) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12 13 89.8 0.2193 0.2197 0.2200 14 12 89.9 0.2566 0.1768 0.2550 13 15 74.0 0.2485 0.3512 0.2500 15 14 58.9 0.2805 0.3427 0.2800 Step 81052, time 1621.04 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 202.120215, max 505.372597 (between atoms 14 and 12) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12 13 79.0 0.2197 70.6136 0.2200 14 12 90.8 0.1768 129.1250 0.2550 13 15 88.6 0.3512 74.7561 0.2500 15 14 90.2 0.3427 114.4250 0.2800 Wrote pdb files with previous and current coordinates Segmentation fault If I change dt = 10 or 15 fs, I am able to run without warnings or segmentation faults up to 300 ns so far even with the same warning: The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 p, which is less than the time step of 1.0e-02 ps. Some details are a bit confusing, is it correct to have backbone bonds with force constants of 150000 without being constrained? This is the default output of the Protein.itp file created by martinize-1.1.py and the value reported in Periole, 2009 ELNEDYN paper. Should I modify the masses of SC or BB beads? My protocol consists of: 1. I use martinize-1.1.py and the specified command options in the tutorial. 2. I do a minimization of the system with position restraints in all beads and stiff bonds for beads in the aromatic side-chains and VAL, MET, THR, SER and so on. (I also performed a short minimization in vacuum with the same conclusions). 3. I do a short equilibration 50 ps with position restraints in all beads and replace stiff bonds by constraints in aromatic beads and some other side-chains (t = 1 fs) 4. I perform 5 ns equilibration with position restraints in backbone beads and dt = 10fs. It fails with dt =20 fs 5. I perform production simulations with dt = 10 – 15 fs. It fails with dt = 20 fs. I am able to run MD using a similar protocol without problems for the same protein with dt = 30 fs without elastic network. Thank you in advance. Jose[file system.top, line 19]:
The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an
estimated oscillational period of 9.7e-02 ps, which is less than 5 times
the time step of 2.0e-02 ps.
Maybe you forgot to change the constraints mdp option.
Should I ignore this warning?
The MD simulation eventually fails with LINCS warning:
Step 81051, time 1621.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.143304, max 0.404759 (between atoms 13 and 15)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
12 13 89.8 0.2193 0.2197 0.2200
14 12 89.9 0.2566 0.1768 0.2550
13 15 74.0 0.2485 0.3512 0.2500
15 14 58.9 0.2805 0.3427 0.2800
Step 81052, time 1621.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 202.120215, max 505.372597 (between atoms 14 and 12)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
12 13 79.0 0.2197 70.6136 0.2200
14 12 90.8 0.1768 129.1250 0.2550
13 15 88.6 0.3512 74.7561 0.2500
15 14 90.2 0.3427 114.4250 0.2800
Wrote pdb files with previous and current coordinates
Segmentation fault
If I change dt = 10 or 15 fs, I am able to run without warnings or segmentation faults up to 300 ns so far even with the same warning:
The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 p, which is less than the time step of 1.0e-02 ps.
Some details are a bit confusing, is it correct to have backbone bonds with force constants of 150000 without being constrained? This is the default output of the Protein.itp file created by martinize-1.1.py and the value reported in Periole, 2009 ELNEDYN paper. Should I modify the masses of SC or BB beads?
My protocol consists of:
1. I use martinize-1.1.py and the specified command options in the tutorial.
2. I do a minimization of the system with position restraints in all
beads and stiff bonds for beads in the aromatic side-chains and VAL, MET, THR, SER and so on. (I also performed a short minimization in vacuum with the same conclusions).
3. I do a short equilibration 50 ps with position restraints in all beads and replace stiff bonds by constraints in aromatic beads and some other side-chains (t = 1 fs)
4. I perform 5 ns equilibration with position restraints in backbone beads and dt = 10fs. It fails with dt =20 fs
5. I perform production simulations with dt = 10 – 15 fs. It fails with dt = 20 fs.
I am able to run MD using a similar protocol without problems for the same protein with dt = 30 fs without elastic network.
Thank you in advance.
Jose
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- xavier
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11 years 10 months ago #974
by xavier
Replied by xavier on topic Elnedyn and time step limit
Dear Jose,
The warning is justified and the reason is that we use a large force constant on the BB-BB bonds originally and left it like this instead of turning it into a constraint. You can ignore the warning.
The reason for your crash can not result from the above warning.
From what residue are the atoms 12, 13, 14, 15 part? A triptophan?
The warning is justified and the reason is that we use a large force constant on the BB-BB bonds originally and left it like this instead of turning it into a constraint. You can ignore the warning.
The reason for your crash can not result from the above warning.
From what residue are the atoms 12, 13, 14, 15 part? A triptophan?
josef wrote: Hello Martini developers,
I have some questions about running an MD simulation of a protein ELNEDYN model with ~ 200 residues solvated in a box of 8 nm size neutralized with 10 NA+. I have revised this and several gromacs forums, but it is not clear how to run MD with dt = 20 fs without the next warning and error:
WARNING 1 : The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 ps, which is less than 5 times the time step of 2.0e-02 ps. Maybe you forgot to change the constraints mdp option. Should I ignore this warning? The MD simulation eventually fails with LINCS warning: Step 81051, time 1621.02 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.143304, max 0.404759 (between atoms 13 and 15) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12 13 89.8 0.2193 0.2197 0.2200 14 12 89.9 0.2566 0.1768 0.2550 13 15 74.0 0.2485 0.3512 0.2500 15 14 58.9 0.2805 0.3427 0.2800 Step 81052, time 1621.04 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 202.120215, max 505.372597 (between atoms 14 and 12) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 12 13 79.0 0.2197 70.6136 0.2200 14 12 90.8 0.1768 129.1250 0.2550 13 15 88.6 0.3512 74.7561 0.2500 15 14 90.2 0.3427 114.4250 0.2800 Wrote pdb files with previous and current coordinates Segmentation fault If I change dt = 10 or 15 fs, I am able to run without warnings or segmentation faults up to 300 ns so far even with the same warning: The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 p, which is less than the time step of 1.0e-02 ps. Some details are a bit confusing, is it correct to have backbone bonds with force constants of 150000 without being constrained? This is the default output of the Protein.itp file created by martinize-1.1.py and the value reported in Periole, 2009 ELNEDYN paper. Should I modify the masses of SC or BB beads? My protocol consists of: 1. I use martinize-1.1.py and the specified command options in the tutorial. 2. I do a minimization of the system with position restraints in all beads and stiff bonds for beads in the aromatic side-chains and VAL, MET, THR, SER and so on. (I also performed a short minimization in vacuum with the same conclusions). 3. I do a short equilibration 50 ps with position restraints in all beads and replace stiff bonds by constraints in aromatic beads and some other side-chains (t = 1 fs) 4. I perform 5 ns equilibration with position restraints in backbone beads and dt = 10fs. It fails with dt =20 fs 5. I perform production simulations with dt = 10 – 15 fs. It fails with dt = 20 fs. I am able to run MD using a similar protocol without problems for the same protein with dt = 30 fs without elastic network. Thank you in advance. Jose[/quote][file system.top, line 19]:
The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an
estimated oscillational period of 9.7e-02 ps, which is less than 5 times
the time step of 2.0e-02 ps.
Maybe you forgot to change the constraints mdp option.
Should I ignore this warning?
The MD simulation eventually fails with LINCS warning:
Step 81051, time 1621.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.143304, max 0.404759 (between atoms 13 and 15)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
12 13 89.8 0.2193 0.2197 0.2200
14 12 89.9 0.2566 0.1768 0.2550
13 15 74.0 0.2485 0.3512 0.2500
15 14 58.9 0.2805 0.3427 0.2800
Step 81052, time 1621.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 202.120215, max 505.372597 (between atoms 14 and 12)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
12 13 79.0 0.2197 70.6136 0.2200
14 12 90.8 0.1768 129.1250 0.2550
13 15 88.6 0.3512 74.7561 0.2500
15 14 90.2 0.3427 114.4250 0.2800
Wrote pdb files with previous and current coordinates
Segmentation fault
If I change dt = 10 or 15 fs, I am able to run without warnings or segmentation faults up to 300 ns so far even with the same warning:
The bond in molecule-type Protein_B between atoms 1 BB and 3 BB has an estimated oscillational period of 9.7e-02 p, which is less than the time step of 1.0e-02 ps.
Some details are a bit confusing, is it correct to have backbone bonds with force constants of 150000 without being constrained? This is the default output of the Protein.itp file created by martinize-1.1.py and the value reported in Periole, 2009 ELNEDYN paper. Should I modify the masses of SC or BB beads?
My protocol consists of:
1. I use martinize-1.1.py and the specified command options in the tutorial.
2. I do a minimization of the system with position restraints in all
beads and stiff bonds for beads in the aromatic side-chains and VAL, MET, THR, SER and so on. (I also performed a short minimization in vacuum with the same conclusions).
3. I do a short equilibration 50 ps with position restraints in all beads and replace stiff bonds by constraints in aromatic beads and some other side-chains (t = 1 fs)
4. I perform 5 ns equilibration with position restraints in backbone beads and dt = 10fs. It fails with dt =20 fs
5. I perform production simulations with dt = 10 – 15 fs. It fails with dt = 20 fs.
I am able to run MD using a similar protocol without problems for the same protein with dt = 30 fs without elastic network.
Thank you in advance.
Jose
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- josef
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11 years 10 months ago #976
by josef
Hi Xavier,
Yes, these atoms belong to a tryptophan. I have noticed that running MD with dt = 20 fs, with a different initial equilibrated configuration, fails with LINCS warnings in the atoms of another TRP in this protein. There are only two TRP's in this system.
Cheers,
Jose
Replied by josef on topic Elnedyn and time step limit
xavier wrote: Dear Jose,
The warning is justified and the reason is that we use a large force constant on the BB-BB bonds originally and left it like this instead of turning it into a constraint. You can ignore the warning.
The reason for your crash can not result from the above warning.
From what residue are the atoms 12, 13, 14, 15 part? A triptophan?
Hi Xavier,
Yes, these atoms belong to a tryptophan. I have noticed that running MD with dt = 20 fs, with a different initial equilibrated configuration, fails with LINCS warnings in the atoms of another TRP in this protein. There are only two TRP's in this system.
Cheers,
Jose
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11 years 10 months ago #977
by xavier
Replied by xavier on topic Elnedyn and time step limit
Ok, this problem has been identified some time ago and fixed but did not make it into the martinize script.
We fixed it in martinize. if you give me an email address I'll send it to you.
XAvier.
We fixed it in martinize. if you give me an email address I'll send it to you.
XAvier.
josef wrote:
xavier wrote: Dear Jose,
The warning is justified and the reason is that we use a large force constant on the BB-BB bonds originally and left it like this instead of turning it into a constraint. You can ignore the warning.
The reason for your crash can not result from the above warning.
From what residue are the atoms 12, 13, 14, 15 part? A triptophan?
Hi Xavier,
Yes, these atoms belong to a tryptophan. I have noticed that running MD with dt = 20 fs, with a different initial equilibrated configuration, fails with LINCS warnings in the atoms of another TRP in this protein. There are only two TRP's in this system.
Cheers,
Jose
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- josef
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11 years 10 months ago #978
by josef
Replied by josef on topic Elnedyn and time step limit
Thank you Xavier, I sent you an e-mail. I will also try with martinize-1.2 released today.
Jose
Jose
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11 years 10 months ago #979
by djurre
Replied by djurre on topic Elnedyn and time step limit
Nothing should change in the Elnedyn parameters when using the version 1.2. The version that Xavier sends you has a quick fix in it. In a next version of the script the changes will be implemented.
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11 years 10 months ago #980
by josef
Replied by josef on topic Elnedyn and time step limit
Thank you! I should wait.
Jose
Jose
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11 years 10 months ago #989
by ascacioc
Replied by ascacioc on topic Elnedyn and time step limit
Hi,
I have exactly the same problem with Trp's. Could you maybe post the martinize.py with the solution online? Alternatively, could I also have this script by email?
Andreea
I have exactly the same problem with Trp's. Could you maybe post the martinize.py with the solution online? Alternatively, could I also have this script by email?
Andreea
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11 years 9 months ago #1053
by jantunes
Replied by jantunes on topic Elnedyn and time step limit
hey,
That fix would be welcomed by me too :P
At the moment I'm running elnedyn with dt = 10fs
Cumps
That fix would be welcomed by me too :P
At the moment I'm running elnedyn with dt = 10fs
Cumps
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