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

Justin A. Lemkul jalemkul at vt.edu
Tue May 26 19:29:35 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?

Were you constraining bond lengths or using position restraints?  You've 
combined the terminology (restraints and constraints are separate ideas in Gromacs).

LINCS warnings and related problems are discussed extensively in the list 
archive (with potential solutions!) as well as on the wiki:


If the problem arises only after adding ions, inspect the location of ion 
insertion.  Since it is random, ions may have been placed in an unfavorable 
location, causing them (or a nearby water molecule) to go careening through the 
simulation cell.  That happened to me once :)


> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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