[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

Justin Lemkul jalemkul at vt.edu
Tue Sep 30 16:36:07 CEST 2014

On 9/30/14 10:30 AM, Anurag Dobhal wrote:
> Dear justin
> Thank you for your rely and precious time.
> I am aware that .gro file is to be visualized in VMD and its content can be
> checked in text editor.
> all the previous .gro file are visualized and checked in VMD.
> I have obetained that ( confout.gro )file by running the command of energy
> minimization i.e.
> "mdrun -v -deffnm em"
> and before this command I ran the command
> "perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat"
> after running the energy minimization the confout.gro is actually obetained as
> confout.gro.trr. so I am renaming it as confout.gro. so it is actually
> .trr format, which can not be visualised in VMD or checked in text
> editor.

Which means it's an invalid input file format and that's why you're getting a 
failure from InflateGRO.  If file names are given different extensions, you 
can't just randomly change them and expect things to work.  If you ran

mdrun -v -deffnm em

you will never get anything named confout.gro.  Note that the tutorial 
explicitly says:

Then, scale down the lipids by a factor of 0.95 (assuming you have used default 
names, the result of the minimization is called "confout.gro"

You didn't use default names.  You told mdrun "name all of my files em.*" when 
you invoked -deffnm.  If you simply ran:

mdrun -s em.tpr

you would get confout.gro.  In any case, you should have "em.gro" which is what 
you should use to proceed.  I have no idea where confout.gro.trr came from, but 
it's a trajectory and clearly not what needs to be used here.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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