[gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"

[Justin Lemkul]

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
>
> Reading.....
> 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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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