[gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

Stefano Meliga smeliga at gmail.com
Tue May 26 19:18:11 CEST 2009

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?


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
> CL-
> (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
> 4AKEallHion.tpr
> $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
> input.
> Thanks a lot,
> Stefano

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