[gmx-users] Re: local pressure v4.5 issues

[Amit Choubey]

Hello Everyone,

The  git version of local pressure calculation at

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

is broken. I could not get it to work for my simulations.

I installed gromacs local pressure version 4.0 from

ftp://ftp.gromacs.org/pub/tmp/

I used gromacs-4.0.2_localpressure.tar.gz<ftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gz>
in
that folder.

The pressure values printed using this version seem reasonable to me. I
converted all the tpr files from v 4.5 to v 4.0.

The output of the mdrun in v 4.0 is a single file "localpressure.dat" . On
the contrary in v 4.5 there were separate "localpressure.dat*" files for
each frame.

I am not sure what exactly is the content of "localpressure.dat". Does it
have the time averaged value of pressure tensor for each voxel ? It doesnt
seem so to me because i tried it over only two frames (3 reruns were done
for two frames separately and a .trr which had these two frames only) and
the numbers did not seem to be averages.

Can someone help me in figuring out what is going on ?

Amit

On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey <kgp.amit at gmail.com> wrote:

>
>
> On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:
>
>> Hi Amit,
>>
>> May I ask you a question?
>> In your calculation of local pressure using a trajectory file, did you get
>> a single averaged localpressure.dat file? Or else you get a bunch of
>> separate files for each frame (e.g., localpressure.dat0, localpressure.dat1,
>> localpressure.dat2 ....)?
>>
>
> Yes I do get different files for different trajectories. All the files seem
> to have the same problem ie a very large/small number printed as tensor
> elements of the pressure for some of the voxels.
>
> Do you have such problems ? Could we compare our methodologies to use the
> local pressure version ?
>
> Amit
>
>>
>> Thank you very much!
>>
>> Cheers,
>> Jianguo
>>
>>
>> ------------------------------
>> *From:* Amit Choubey <kgp.amit at gmail.com>
>> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
>> *Sent:* Monday, 20 June 2011 07:08:03
>> *Subject:* [gmx-users] Re: local pressure v4.5 issues
>>
>> Dear all,
>>
>> I did another simulation with only SPC water. Then I used the local
>> pressure gromacs to calculate the stresses. It seems to be reasonable.
>>
>> I am not sure how to figure out what goes wrong with my previous
>> simulations when plugged into the local pressure gromacs.
>>
>> Could someone help me in figuring out whats the issue ?
>>
>> Thank You.
>>
>> On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey <kgp.amit at gmail.com> wrote:
>>
>>> Dear all,
>>>
>>> I installed the git version of local pressure calculation from
>>>
>>>
>>> http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
>>>
>>> The I invoked mdrun
>>>
>>> mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid
>>> 0.1
>>>
>>> This created a file named "localpressure.dat0". This is a binary file so
>>> I could not look at it directly. I am not sure if there is a tool in the
>>> gromacs to look at it directly.
>>>
>>> To look at the data in "localpressure.dat0" I used the planar_av.c code
>>> available in "pressure-tools" folder at
>>>
>>> http://md.chem.rug.nl/cgmartini/index.php/3d
>>>
>>> When I look at the Pressure tensor averaged over xy plane, some of the
>>> numbers are reasonable but few of them are ridiculously large numbers which
>>> is not expected.
>>>
>>> I checked this on two different simulations and I got the same problems.
>>> The simulations had run OK previously.
>>>
>>> Could someone help me in figuring our whats going on ?
>>>
>>> Amit Choubey
>>>
>>>
>>
>
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