[gmx-users] Regarding GROMACS Tutorial "KALP15 in DPPC"
anurag.dobhal at nano-medicine.co.in
Mon Sep 29 10:44:55 CEST 2014
Can you please tell me how will i solvate my system.
which command will i use and what will be my input and output file.
Thanks for your help
On Sun, Sep 28, 2014 at 6:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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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