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

[Anurag Dobhal]

hello justin

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

Anurag dobhal

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
>>
>> 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
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> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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