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

Stefano Meliga smeliga at gmail.com
Tue May 26 18:41:13 CEST 2009

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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