[gmx-users] Problems with Ion

Justin Lemkul jalemkul at vt.edu
Fri Nov 21 03:38:45 CET 2014

On 11/20/14 3:55 PM, Fábio Filippi Matioli wrote:
> I basically do what the guide indicates...
> I Run this command (pasted down) to generate the pdb with the ion on correct place and no jumps on box, but the output its different when compared with the after.gro generated after de MD on mdrun command
> Command:
> trjconv -pbc nojump -f full2.trr -s full.tpr -o after_full_2.pdb -b 50000 -e 50000

This will of course be different because you are performing a periodicity 
operation on the file.

> I putted this timed after -b and -e because I would like only the pdb with the last state of the MD, equal the after.gro

It is easier and more reliable to use -dump 50000 rather than setting -b and -e 
to the same value.



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


More information about the gromacs.org_gmx-users mailing list