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

[Amit Choubey]

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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