[gmx-users] problem with water models in Gromacs 5.1.2
jalemkul at vt.edu
Sun Mar 6 17:27:09 CET 2016
On 3/4/16 4:04 PM, Irem Altan wrote:
> It turns out that my problems with TIP5P were more general than I thought. I recently switched from version 4.6.5, with which I could run simulations using AMBER99SB + (SPC, SPC/E, TIP4P, TIP3P). I decided to do the following test:
> 1- I created a .pdb file with a single calcium ion, within a cubic unit cell of side 30 A:
> CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 1
> HETATM 1 CA CA A 1 32.702 -10.496 -5.429 1.00 12.22 CA
> 2- I then run pdb2gmx and select amber99sb and SPC (I tried it with TIP4P as well):
> gmx pdb2gmx -f test.pdb -o box.gro -p topol.top
> 3- I run solvate:
> gmx solvate -cp box.gro -cs spc216 -p topol.top -o box_h2o.gro
> 4- then I substitute some waters with sodium and chloride ions:
> gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top
> gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05
> 5- Energy minimization (this is where things go horribly wrong):
> gmx grompp -f minim.mdp -p topol.top -c ions.gro -o em.tpr
> gmx mdrun -v -deffnm em
> Then the following error appears:
> Fatal error:
> step 11: Water molecule starting at atom 86 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> I’m guessing there is something that changed from version 4.6.5 to 5.1.2 that I can’t pinpoint. What could I be overlooking? (The contents of my .mdp files are below)
Do the regression tests pass on your installation? A box of water and ions
should not fail in any GROMACS version, ever.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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