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

[Amit Choubey]

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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