[gmx-users] Energy minimisation step in Lipid protein simulation

[Balasubramanian Suriyanarayanan]

But is not "confout.gro" the output of the compression step.

the command is
"perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat"

or else what is the output of above command.

regards

suriyanarayanan





On Thu, Jun 12, 2014 at 3:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/12/14, 4:54 AM, Balasubramanian Suriyanarayanan wrote:
>
>> Dear friends, In protein lipid simulation , when I do energy minimisation
>> ster I get an error as " Eeeeek! No confout.gro at all!
>>
>>                 Died at inflategro.pl line 104."
>>
>> What is "confout.gro". If am right it is the output file that we get from
>> the minimisation step.
>>
>> I used the command " perl inflategro.pl confout.gro 0.95 POPC 0
>> system_shrink1.gro 5 area_shrink1.dat".
>>
>>
> You're specifying confout.gro as the source of coordinates.  Apparently
> that file doesn't exist in the working directory, so InflateGRO is giving
> you an error.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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