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

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 27 04:16:56 CEST 2009

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.


> Thanks,
> Stefano.
> 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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