[gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"
jalemkul at vt.edu
Sun Sep 28 15:28:41 CEST 2014
On 9/28/14 9:14 AM, Anurag Dobhal wrote:
> Hey gromacs users
> I got the confout.gro file by running the command
> mdrun -v -deffnm em -o confout.gro
> and then i ran the command " perl inflategro.pl confout.gro 0.95 DPPC
> 0 system_shrink1.gro 5 area_shrink1.dat "
> but now the teminal says that
> Use of uninitialized value $box_x in multiplication (*) at
> inflategro.pl line 339.
> Use of uninitialized value $box_y in multiplication (*) at
> inflategro.pl line 340.
> Scaling lipids....
> There are 0 lipids...
> Illegal division by zero at inflategro.pl line 380
> is this output is expected ???
No, fatal errors like that are not expected. If EM successfully completed and
wrote a confout.gro file, there should be no problem. Visualize confout.gro and
make sure its contents are sane.
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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