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Minimization and equilibration membrane proteins
- Robin
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7 years 10 months ago #5619
by Robin
Minimization and equilibration membrane proteins was created by Robin
Hi,
I'm doing a membrane protein simulation with martini 22 for the lipids (created using insane.py) and elnedyn 22. The objective of this simulation is to observe dimerization of the 2 proteins.
In order to insert the two protein at a distance of 10 nm from each other, I used vmd to move one protein, and then merged the 2 .gro file into one before renumbering the atoms. The 2 proteins where inserted as if they were only one with insane.py.
I minimized the structure with the following parameters:
define = -DPOSRES
integrator = steep
nsteps = 150000
energygrps = W_NA+_CL- Protein_POPC_CHOL
nstlist = 1
ns_type = grid
rlist = 1.4
coulombtype = Shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
constraints = none
pbc = xyz
cutoff-scheme = group
Which interrupted with the following message:
Steepest Descents converged to machine precision in 31818 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -8.6182638e+05
Maximum force = 3.2809598e+02 on atom 1144
Norm of force = 7.1021566e+00
Can you tell me if it's an error? I did check that atoms and didn't find any abnormality/overlapping atom.
Seeing the minimization converged anyway, I did equilibration with the following parameters:
define = -DPOSRES
integrator = md
dt = 0.01
nsteps = 50000
nstcomm = 100
nstxout = 1000
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 100
nstxout-compressed = 100
compressed-x-precision = 100
energygrps = W_NA+_CL- Protein_POPC_CHOL
cutoff-scheme = group
nstlist = 10
rlist = 1.4
coulombtype = Shift
;rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = W_NA+_CL- Protein_POPC_CHOL
tau_t = 1.0 1.0
ref_t = 310 310
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = yes
gen_temp = 310
gen_seed = -1
refcoord_scaling = all
Since I didn't find any consensus on equilibration parameters for systems similars to mine, could you please tell me if you think those parameters are liable?
Moreover, during the equilibration, the squared membrane (from upper view) began somewhat round, is it problematic?
Please excuse me if my questions are trivials, i'm pretty new in gromacs and martini.
I'm doing a membrane protein simulation with martini 22 for the lipids (created using insane.py) and elnedyn 22. The objective of this simulation is to observe dimerization of the 2 proteins.
In order to insert the two protein at a distance of 10 nm from each other, I used vmd to move one protein, and then merged the 2 .gro file into one before renumbering the atoms. The 2 proteins where inserted as if they were only one with insane.py.
I minimized the structure with the following parameters:
define = -DPOSRES
integrator = steep
nsteps = 150000
energygrps = W_NA+_CL- Protein_POPC_CHOL
nstlist = 1
ns_type = grid
rlist = 1.4
coulombtype = Shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
constraints = none
pbc = xyz
cutoff-scheme = group
Which interrupted with the following message:
Steepest Descents converged to machine precision in 31818 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -8.6182638e+05
Maximum force = 3.2809598e+02 on atom 1144
Norm of force = 7.1021566e+00
Can you tell me if it's an error? I did check that atoms and didn't find any abnormality/overlapping atom.
Seeing the minimization converged anyway, I did equilibration with the following parameters:
define = -DPOSRES
integrator = md
dt = 0.01
nsteps = 50000
nstcomm = 100
nstxout = 1000
nstvout = 0
nstfout = 0
nstlog = 100
nstenergy = 100
nstxout-compressed = 100
compressed-x-precision = 100
energygrps = W_NA+_CL- Protein_POPC_CHOL
cutoff-scheme = group
nstlist = 10
rlist = 1.4
coulombtype = Shift
;rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = W_NA+_CL- Protein_POPC_CHOL
tau_t = 1.0 1.0
ref_t = 310 310
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = yes
gen_temp = 310
gen_seed = -1
refcoord_scaling = all
Since I didn't find any consensus on equilibration parameters for systems similars to mine, could you please tell me if you think those parameters are liable?
Moreover, during the equilibration, the squared membrane (from upper view) began somewhat round, is it problematic?
Please excuse me if my questions are trivials, i'm pretty new in gromacs and martini.
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- mnmelo
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7 years 10 months ago #5622
by mnmelo
Replied by mnmelo on topic Minimization and equilibration membrane proteins
Hello Robin,
Your minimization seems ok. That message is the indication that it converged. In your case, the reported maximum force and pot. energy are ok.
You can increase nstlist to 10 when minimizing, and 5000 steps should be enough (150000 are definitely way too many).
As to your equilibration, the membrane becoming round *is* problematic. There's not much info on your system, but here's some tips that might help:
- You're inserting two proteins using insane.py. IIRC insane.py might need the -ring flag to properly insert lipids in-between the proteins. Do check if you're getting a reasonable lipid placement even before minimization.
- In your equilibration you are using refcoord_scaling = all. This will distort the proteins as the membrane equilibrates its area. Use refcoord_scaling = com
(this is still not ideal for your case, but you have no better option. Read the refcoord_scaling documentation).
Good luck,
Manel
Your minimization seems ok. That message is the indication that it converged. In your case, the reported maximum force and pot. energy are ok.
You can increase nstlist to 10 when minimizing, and 5000 steps should be enough (150000 are definitely way too many).
As to your equilibration, the membrane becoming round *is* problematic. There's not much info on your system, but here's some tips that might help:
- You're inserting two proteins using insane.py. IIRC insane.py might need the -ring flag to properly insert lipids in-between the proteins. Do check if you're getting a reasonable lipid placement even before minimization.
- In your equilibration you are using refcoord_scaling = all. This will distort the proteins as the membrane equilibrates its area. Use refcoord_scaling = com
(this is still not ideal for your case, but you have no better option. Read the refcoord_scaling documentation).
Good luck,
Manel
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- Robin
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7 years 10 months ago - 7 years 10 months ago #5624
by Robin
Replied by Robin on topic Minimization and equilibration membrane proteins
Hello Mnmelo,
Thank you very much for your quick answer. I can finally stop worrying about minimization.
About equilibration:
- The membrane area is becoming a circle (not globular) compared to the squared starting structure, but the 2 water layers and lipid bilayers only got thicker (more dense). The area (from upper view of the membrane) should keep the original square form during thickening? Edit: it happens only at the beginning of equilibration, the membrane area go back to square form after 50 000 steps. Maybe a pressure issue?
- I did use the -ring option, with the following command:
python insane.py -f MORDOR100.gro -o popchol20MORDOR.gro -p popchol20MOR.top -pbc square -box 20,20,10 -l POPC:10.0 -l CHOL:1.0 -center -sol W -salt 0.15 -ring -charge auto
The lipid placement seems reasonable.
- I'm currently trying with the refcoord_scaling=com. Thank you for the suggestion, as you say the thickening of the membrane probably extend my protein with the option all.
- Finally, are pressure, temperature, volume stabilisation, and protein rmsd enough criterias for admitting the equilibration is finished ?
Thank you very much for your quick answer. I can finally stop worrying about minimization.
About equilibration:
- The membrane area is becoming a circle (not globular) compared to the squared starting structure, but the 2 water layers and lipid bilayers only got thicker (more dense). The area (from upper view of the membrane) should keep the original square form during thickening? Edit: it happens only at the beginning of equilibration, the membrane area go back to square form after 50 000 steps. Maybe a pressure issue?
- I did use the -ring option, with the following command:
python insane.py -f MORDOR100.gro -o popchol20MORDOR.gro -p popchol20MOR.top -pbc square -box 20,20,10 -l POPC:10.0 -l CHOL:1.0 -center -sol W -salt 0.15 -ring -charge auto
The lipid placement seems reasonable.
- I'm currently trying with the refcoord_scaling=com. Thank you for the suggestion, as you say the thickening of the membrane probably extend my protein with the option all.
- Finally, are pressure, temperature, volume stabilisation, and protein rmsd enough criterias for admitting the equilibration is finished ?
Last edit: 7 years 10 months ago by Robin.
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- mnmelo
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- Posts: 89
7 years 10 months ago #5626
by mnmelo
Replied by mnmelo on topic Minimization and equilibration membrane proteins
If your membrane is periodic in xy (as it should be, based on your input) it should always remain a square. Otherwise, what is taking its place at the corners of your box?
Manel
Manel
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- Robin
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7 years 10 months ago - 7 years 10 months ago #5630
by Robin
Replied by Robin on topic Minimization and equilibration membrane proteins
Hi Manel,
In fact, my membrane is periodic in xyz (can't use xy with my parameters or I got this error ERROR 1 : Can not have pressure coupling with pbc=xy). Looking at the periodic display in vmd (+x, +y, +z) I see at the beginning that their is about 1nm vacuum in each direction between each periodic image. Seems right since I used the command gmx editconf -f popchol20prots.gro -d 1.0 -o prots100newbox.gro as advised in the martini protein tutorial. The membrane area deformation is happening at the beginning of the equilibration (at about 0.2 ns), and quicly moving in order to fill this vaccuum. However, as soon as the vaccuum between the periodic images is filled with the membrane (extending for that purpose), the area stays squared until the end of the 5ns simulation. I'm starting to think it's only normal during the temperature and pressure stabilisation of the system.[file equilibrationberendsen.mdp]:
Can not have pressure coupling with pbc=xy).
Looking at the periodic display in vmd (+x, +y, +z) I see at the beginning that their is about 1nm vacuum in each direction between each periodic image. Seems right since I used the command gmx editconf -f popchol20prots.gro -d 1.0 -o prots100newbox.gro as advised in the martini protein tutorial. The membrane area deformation is happening at the beginning of the equilibration (at about 0.2 ns), and quicly moving in order to fill this vaccuum. However, as soon as the vaccuum between the periodic images is filled with the membrane (extending for that purpose), the area stays squared until the end of the 5ns simulation. I'm starting to think it's only normal during the temperature and pressure stabilisation of the system.
In fact, my membrane is periodic in xyz (can't use xy with my parameters or I got this error ERROR 1 : Can not have pressure coupling with pbc=xy). Looking at the periodic display in vmd (+x, +y, +z) I see at the beginning that their is about 1nm vacuum in each direction between each periodic image. Seems right since I used the command gmx editconf -f popchol20prots.gro -d 1.0 -o prots100newbox.gro as advised in the martini protein tutorial. The membrane area deformation is happening at the beginning of the equilibration (at about 0.2 ns), and quicly moving in order to fill this vaccuum. However, as soon as the vaccuum between the periodic images is filled with the membrane (extending for that purpose), the area stays squared until the end of the 5ns simulation. I'm starting to think it's only normal during the temperature and pressure stabilisation of the system.[file equilibrationberendsen.mdp]:
Can not have pressure coupling with pbc=xy).
Looking at the periodic display in vmd (+x, +y, +z) I see at the beginning that their is about 1nm vacuum in each direction between each periodic image. Seems right since I used the command gmx editconf -f popchol20prots.gro -d 1.0 -o prots100newbox.gro as advised in the martini protein tutorial. The membrane area deformation is happening at the beginning of the equilibration (at about 0.2 ns), and quicly moving in order to fill this vaccuum. However, as soon as the vaccuum between the periodic images is filled with the membrane (extending for that purpose), the area stays squared until the end of the 5ns simulation. I'm starting to think it's only normal during the temperature and pressure stabilisation of the system.
Last edit: 7 years 10 months ago by Robin. Reason: for clarity
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