[gmx-users] Lateral pressure profile in membrane simulations

[Martti Louhivuori]

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