[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
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
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
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
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