[gmx-users] Re: solution molecules cannot be set by mdrun after neutralization
smeliga at gmail.com
Wed May 27 19:10:38 CEST 2009
My integrator is "steep", which should perform EM.
This is my mdp file:
title = 4AKE_PREMsteep
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = all-bonds
integrator = steep
nsteps = 500
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
DispCorr = no
; Energy minimizing stuff
emtol = 1.0
emstep = 0.01
I learnt from the tutorials (s-peptide) that in order to do a position
restrained MD the I have to set the constraints (all-bonds in this case).
Is that incorrect? Is it valid for EM as well?
Thank you for your advice,
Mark Abraham ha scritto:
> Stefano Meliga wrote:
>> Hi again,
>> I've tryed to perform the same preprocessing and EM steps without
>> distance constraints and the situation improves a lot.
>> I get no warnings in the steepest descent EM and only one molecule
>> cannot be set in the conjugate gradient EM.
>> Can you see the reason?
> Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your
> integrator in your .mdp file better.
> Also, as Justin suggests, please be careful with the
> constraint/restraint terminology.
>> Stefano Meliga ha scritto:
>>> Hi everybody,
>>> I neutralized my system with the commands:
>>> $grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p
>>> 4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
>>> $grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
>>> 4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname
>>> (adding the atoms to the solution SOL)
>>> I renamed the files to keep track of the different topology files:
>>> mv 4AKEallHsol_pre.top 4AKEallHion.top
>>> mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top
>>> I run an all-bonds position restraint steepest descent EM:
>>> $grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
>>> 4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
>>> $grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
>>> 4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v
>>> mdrun exits successfully but displays the warning:
>>> t = 0.011 ps: Water molecule starting at atom 17223 can not be settled.
>>> Check for bad contacts and/or reduce the timestep.
>>> In the gro file atom 17223 is an oxigen of the solution
>>> Going further with my simulation i run a all-bonds position restrained
>>> conjugate gradient EM:
>>> $grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
>>> 4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top
>>> -o 4AKEallH_PREMsteep.tpr
>>> $grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
>>> 4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v
>>> but get the fatal error:
>>> Source code file: constr.c, line: 136
>>> Fatal error:
>>> Too many LINCS warnings (2200)
>>> And some of this warnings are again solution's molecules that cannot
>>> be set.
>>> May the problem be related to the ions added to neutralise the system?
>>> mdrun was not showing this problem with the non-neutral system in
>>> Thanks a lot,
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