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

[Amit Choubey]

On Wed, Sep 7, 2011 at 12:30 AM, Shou-Chuang Yang <shcyang at ucdavis.edu>wrote:

>
>
> 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.
>

Why do you get a segmentation fault if you swap the y and z
coordinates,velocity columns?

Another way around is to change the simple_localpres_analysis.c code. If you
look into it there is a loop that runs over boxes in z direction to
calculate pressure tensor in z direction. You could change it to y.


> 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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