[gmx-users] Lateral pressure profile in membrane simulations

[George Khelashvili]

Thank you!

I will follow your guidelines.

George

XAvier Periole wrote:
>
> 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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>


-- 
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
gek2009 at med.cornell.edu
Phone: 1-212-746-6539
Fax:   1-212-746-6226