You have to rerun the trajectory ... not frame by frame!
Notes:
- that there is issue on pressure tensor calculation when constrains are
used
- simulations need to be quite long to get a reasonable convergence.
On Apr 12, 2010, at 2:41 AM, George Khelashvili wrote:
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: gek2...@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: gek2...@med.cornell.edu
phone: 1-212-746-6539
fax: 1-212-746-6226
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