[gmx-users] Gro file does not match topology file... continue

Justin Lemkul jalemkul at vt.edu
Sat Jan 28 02:45:07 CET 2017

On 1/27/17 8:39 PM, Tasneem Kausar wrote:
> Yes , you are right. I was also surprised that when atoms in gro and
> topology match then how this error can be.
> In my case I was simulating a small peptide segment in water. Everything
> goes smoothly in it. Then I have generated a system with 8 peptides using
> genconf command.
> I have generated a box with editconf with -d 1.1 in a cubical box. In last
> line of topology file protein_chain_A was changed from 1 to 8. The genbox
> was used to solvate the system. Then grompp gives  the mismatch error.
> Then with a box size of 2.1grompp was executed without any error.
> Same mdp file was used in both the case.
> This is the whole procedure, I have followed.
> This is why I was saying to increase the box size.

Without exact commands and error messages, there's no way to know what happened 
except that whatever mistake you made the first time, you didn't make the 
second.  "Increase the box size" is not a solution for a mismatch between 
coordinates and topology.  Correct bookkeeping is.



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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