[gmx-users] problem with water models in Gromacs 5.1.2

[Irem Altan]

Hi,

Yes, the tests were performed. It turns out that I had to reduce the energy step size during minimization. Thank you.

Best,
Irem

> On Mar 6, 2016, at 11:27 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 3/4/16 4:04 PM, Irem Altan wrote:
>> Hi,
>> 
>> 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:
>> 
>> (test.pdb)
>> 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
> 
> -- 
> ==================================================
> 
> 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
> http://mackerell.umaryland.edu/~jalemkul
> 
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