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
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