[gmx-users] adding polyatomic species in water

Justin Lemkul jalemkul at vt.edu
Wed Feb 4 14:18:23 CET 2015

On 2/4/15 5:10 AM, #SUKRITI GUPTA# wrote:
> Dear Gromacs Users,
> I am trying to simulate a cell containing different polyatomic species like sulphate, glucose, acetic acid etc. in water. I start my simulation by taking pdb file containing 1 sulphate ion and then add remaining sulphate ions and other species using -cs and -ci from genbox. I use genbox command multiple time till all the species are added and system is solvated in water. But when I perform energy minimisation, the initial system starts with a very high energy i.e. around 10^6 range and the either it doesn't get converged or i get msg Segmentation fault (core dumped).
> I also tried using genconf but still i was getting the same problem.
> Can anyone please let me know what is wrong with my system and how can i correctly add all the species in my system.

Your approach for building the system is correct.  mdrun will print the atom on 
which the maximum force acts, so that should be your first point of inspection. 
  The failures you're describing indicate either unresolvable atomic clashes 
(maybe try a new value of -vdwd when building the system) or bad topology.



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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