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reverse transformation of acylated and amidaded peptides
- nanogod
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11 years 2 months ago #1410
by nanogod
reverse transformation of acylated and amidaded peptides was created by nanogod
Hey,
I have a problem with converting a CG simulation containing peptides with no termini charges. What I have done was run a CG simulation using martini 2.2P and after the MD simulation remove all beads not contained in martini 2.2, remove WM and WP and rename PW to W. I have done the same with a simulation where the termini of the peptides were charged, but when using the same peptide without termini charges I encounter a problem. My fg structure of the md simulations looks fine, but after mdrun it responds with the following error:
Warning: 1-4 interaction between 70 and 86 at distance 3.391 which is larger than the 1-4 table size 1.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
Back Off! I just backed up traj.trr to ./#traj.trr.4#
Back Off! I just backed up traj.xtc to ./#traj.xtc.3#
step 0
Program 33_mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 539 ]
Please report this to the mailing list (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Does anyone have an explantion? I have tried minimizing the cg structure before transforming it to fg and I have tried using editconf with -pbc to make molecules whole
Kind regards
Nanogod
I have a problem with converting a CG simulation containing peptides with no termini charges. What I have done was run a CG simulation using martini 2.2P and after the MD simulation remove all beads not contained in martini 2.2, remove WM and WP and rename PW to W. I have done the same with a simulation where the termini of the peptides were charged, but when using the same peptide without termini charges I encounter a problem. My fg structure of the md simulations looks fine, but after mdrun it responds with the following error:
Warning: 1-4 interaction between 70 and 86 at distance 3.391 which is larger than the 1-4 table size 1.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
Back Off! I just backed up traj.trr to ./#traj.trr.4#
Back Off! I just backed up traj.xtc to ./#traj.xtc.3#
step 0
Program 33_mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 539 ]
Please report this to the mailing list (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Does anyone have an explantion? I have tried minimizing the cg structure before transforming it to fg and I have tried using editconf with -pbc to make molecules whole
Kind regards
Nanogod
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- nanogod
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11 years 2 months ago #1411
by nanogod
Replied by nanogod on topic reverse transformation of acylated and amidaded peptides
Might I also add, when removing all other molecules but one peptide, the transformation proceeds without any problems
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- xavier
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11 years 1 month ago #1432
by xavier
Replied by xavier on topic reverse transformation of acylated and amidaded peptides
I assume that by removing the particle not present in 2.2 you mean in the trajectory. Did you generate a new tpr file or you use the previous one? If you had one without polarizable stuff. Then I would think that the problem comes from mismatch between the tpr and the coordinate.
The problem can not be the inclusion or exclusion of termini charges ... it must be something funky done in the procedure ...
The problem can not be the inclusion or exclusion of termini charges ... it must be something funky done in the procedure ...
nanogod wrote: Hey,
I have a problem with converting a CG simulation containing peptides with no termini charges. What I have done was run a CG simulation using martini 2.2P and after the MD simulation remove all beads not contained in martini 2.2, remove WM and WP and rename PW to W. I have done the same with a simulation where the termini of the peptides were charged, but when using the same peptide without termini charges I encounter a problem. My fg structure of the md simulations looks fine, but after mdrun it responds with the following error:
Warning: 1-4 interaction between 70 and 86 at distance 3.391 which is larger than the 1-4 table size 1.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
Back Off! I just backed up traj.trr to ./#traj.trr.4#
Back Off! I just backed up traj.xtc to ./#traj.xtc.3#
step 0
Program 33_mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 539 ]
Please report this to the mailing list (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Does anyone have an explantion? I have tried minimizing the cg structure before transforming it to fg and I have tried using editconf with -pbc to make molecules whole
Kind regards
Nanogod
Please Log in or Create an account to join the conversation.
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