[gmx-users] 3D pressure profile of a bilayer

[Shou-Chuang Yang]

On Wed, Sep 7, 2011 at 12:11 AM, Amit Choubey <kgp.amit at gmail.com> wrote:

>
>
> On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang <shcyang at ucdavis.edu>wrote:
>
>> Dear gmx-users,
>>
>> Could anyone help me with the calculation of 3D pressure profile in a
>> function of y?
>> I used the provided gromacs-4.0.2_localpressure for my calculatioin. It
>> calculate
>> the 3D pressure profile as a function of z (the default setting of bilayer
>> normal
>> is z-direction).
>>
>> In my case, I have a bilayer which rotate at the first few nano second run
>> and remained normal to y-directiona for the rest. How can I obtain a 3D
>> pressure analysis
>> along the y-direction?
>>
> Couldnt you rotate your box so that the bilayer is in z dir ?
>

The local pressure analysis need to read the trajectory file with both
positions and velocities.
I thought of rotate my system and rerun it for the last 600 ns ( I am using
MARTINI), but since
I am also doing semiisotropic coupling, I cannot "rotate" the pressure
coupling directions.

Another way I tried is to modify the output .trr into another .trr which y
and z columns printed out
reversely as well as the Vy and Vz columns. Thinking that maybe the analysis
code will read my
"originally y coordinates" as "z coordinates". What I got was segmentation
fault.
I am not sure whether it will work out eventually.

> I really appreciated your help!
>>
>> Thanks,
>> Joanne
>> --
>>
>>
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>
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-- 
Shou-Chuang Yang
Master’s Candidate
Department of Chemical Engineering and Materials Science
University of California, Davis
Phone: 1-646-639-4240
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