[gmx-users] Lateral pressure profile in membrane simulations

[XAvier Periole]

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: 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
>
> -- 
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