[gmx-users] Simulating Multiple Solute Particles

Justin Lemkul jalemkul at vt.edu
Wed Nov 12 13:48:22 CET 2014

On 11/12/14 2:58 AM, Nathan K Houtz wrote:
> Dr. Lemkul,
> Thank you again - your tutorials are very helpful for me. I want to get through your Virtual Sites tutorial but I got stuck near the beginning. Gromacs thinks the minim.mdp file is for an earlier version but the introduction page said it's for 5.0 and later. I'm using gromacs 5.0.2, so I thought I should be fine. I copied this command:
>> gmx grompp -f minim.mdp -c box.pdb -p topol.top -o min.tpr
> after having made my box, of course, and got the following error:
>> Command line:
>>   gmx grompp -f minim.mdp -c box.pdb -p topol.top -o min.tpr
>> NOTE 1 [file minim.mdp, line 19]:
>>   minim.mdp did not specify a value for the .mdp option "cutoff-scheme".
>>   Probably it was first intended for use with GROMACS before 4.6. In 4.6,
>>   the Verlet scheme was introduced, but the group scheme was still the
>>   default. The default is now the Verlet scheme, so you will observe
>>   different behaviour.
>> Ignoring obsolete mdp entry 'title'
>> ERROR 1 [file minim.mdp]:
>>   With Verlet lists only full pbc or pbc=xy with walls is supported
>> ERROR 2 [file minim.mdp]:
>>   With Verlet lists nstlist should be larger than 0
>> NOTE 2 [file minim.mdp]:
>>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>>   your simulation.
> I tried to figure out how I could modify it myself but I don't really know what I'm doing. The sample mdp file (http://manual.gromacs.org/online/mdp.html) is much longer than the one you linked (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/Files/minim.mdp) and I'm not sure which fields are necessary. Is the file outdated, or have I made a mistake?

Setting "cutoff-scheme = group" should fix this.  I'll fix the tutorial.  I 
guess that change slipped through the cracks.



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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