[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

Anurag Dobhal anurag.dobhal at nano-medicine.co.in
Fri Oct 3 12:21:30 CEST 2014

hello Justin thanks for your reply.

I am unable to understand how to proceed in this tutorial. I am working on
it from many days but I am unable to do.

I have understood till the step.

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat

this is the result which I got.

Area per protein: 2 nm^2
Area per lipid: 10.4716089904762 nm^2

Area per protein, upper half: 1.75 nm^2
Area per lipid, upper leaflet : 10.4755772444444 nm^2

Area per protein, lower half: 2 nm^2
Area per lipid, lower leaflet : 10.4716089904762 nm^2

Writing Area per lipid...

and the minimization step after that. I get the confout.gro file.

I am confused how to continue from the step

"perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5

how many times do we need to run this command, nd with what changes ????

and how to solvate the system  ( which file ) and what will be the command ???

looking for your kind reply.

please help.

Thank you

On Thu, Oct 2, 2014 at 10:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 10/2/14 12:51 PM, Anurag Dobhal wrote:
>> how will I get to know that the system have shrunken enough, and which
>> file
>> I need to solvate.
> This is stated in the tutorial.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
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