[gmx-users] Simulation of membrane protein

James Starlight jmsstarlight at gmail.com
Mon Oct 31 16:30:36 CET 2011

Thanks, Justin
I'll test your program soon.

Today also I have some problems with generation of the posre for lipids

I have lipid bilayer in pdb. Then I selected one lipid molecule and move it
to  separate pdb and convert it to gro via editconf.
Than I've used genres and generate posre file for 1 lipid. Than I include
tis posre to topology of my bilayer
using gropt I obtain eror that I'm using wrong posre topology

Also I've tried to include posre.itp to my lipid.itp ( this file contain
link to posre on default) This run didnt produce any errors but as the
result posres have not been worked ( I obtained perturbed bilayer after

How I can generate work posre for my bilayer to prevent perturbation after
equilibration or minimization ?


2011/10/31 Justin A. Lemkul <jalemkul at vt.edu>

> James Starlight wrote:
>> In some papers I found Gromacs graphs showed indirectly measurements of
>> the time evolution of the Area per lipid value. What gromac's program could
>> be used for it for cheacking the above value during simulation runs ?
> There is no Gromacs tool for this.  For a simple membrane system, one can
> use g_energy to extract box vectors over time, which can then be divided by
> the number of lipids per leaflet to extract the APL.  For systems with
> proteins embedded in membranes, it is no trivial exercise to make such
> measurements.  We wrote a program several years ago that calculates APL for
> such systems:
> http://www.bevanlab.biochem.**vt.edu/GridMAT-MD/<http://www.bevanlab.biochem.vt.edu/GridMAT-MD/>
> The program can only be run on single snapshots at the moment, but you can
> assemble time evolution from the output.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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