[gmx-users] Lateral pressure profile in membrane simulations

[George Khelashvili]

Dear users,

I am attempting to perform 3D pressure tensor calculation on 
well-converged all-atom lipid bilayer. I am using modified gromacs and 
-rerun option and analyze the output with the tools that is provided on 
Martini website. I had following question: I have a production 
trajectory from original MD calculations, and I also have separate 
snapshots saved once in 100ps. As I understand, for pressure 
calculations I need to use -rerun on separate snapshots. Is this the 
case? If so, I would get as an output bunch of local_pressure.dat files. 
How do I analyze them? One by one? I would greatly appreciate if 
somebody can describe the sequence of events that I need to go through 
in order to obtain pressure profiles.

Thank you for you assistance,

Sincerely,
George

-- 
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
e-mail: gek2009 at med.cornell.edu
phone:  1-212-746-6539
fax:    1-212-746-6226


Martti Louhivuori wrote:
> On 8 Apr 2010, at 00:45, Fernando E. Herrera wrote:
>> I am doing some molecular dynamics simulations of membrane systems 
>> and i would like to ask you if someone know or have a code for the 
>> calculation of the lateral pressure profile  from the data obtained 
>> doing  membrane simulations.
>
> You can find everything you need from here:
> http://www.cgmartini.nl/index.php/tools/114-3d-pf
>
> It is a custom version of Gromacs that calculates a 3D pressure field 
> using the -rerun option of mdrun, as explained in Ollila et al. (2009) 
> PhysRevLett 102: 078101. Before you do the rerun, you need to redo 
> grompp with 'userreal1' set to the desired grid size. The analysis 
> tools there can then be used to calculate e.g. a lateral pressure 
> profile... Note that constraints are a bit problematic, though, so if 
> your lipids have constraints, the profile may not be accurate.
>
> Best regards,
> -martti-
> -- 
> Post-doctoral research fellow
> Moleculaire Dynamica
> University of Groningen
> Nijenborgh 4, 9747AG Groningen, the Netherlands
> tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398
>


-- 
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
e-mail: gek2009 at med.cornell.edu
phone:  1-212-746-6539
fax:    1-212-746-6226