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

[Amit Choubey]

On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:

> Hi Amit,
>
> I also encountered the same problem you mentioned.
> In v4.5, when using -nstlp wiht large value (e.g., 10000000), I got one
> file "localpressure.dat0". I tested first several frames of a trajectory,
> the calculated pressure is not the average of the pressure of individual
> frames.
>
>

In v4.5 it outputs the profile for frames in separate files which is ok. My
concern is what exactly is going in v 4.0 where there is only one file for
all the frames.

Also where did you download v4.5 and v4.0 from ?


> Btw, did you use CHARMM FF in your simulations and how did you convert the
> tpr files from v 4.5 to v 4.0?
>

Yes i have used CHARMM FF and i will have to figure out the conversion.

>
> Cheers
> Jianguo
>
> ------------------------------
> *From:* Amit Choubey <kgp.amit at gmail.com>
> *To:* Jianguo Li <ljggmx at yahoo.com.sg>; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> *Sent:* Friday, 1 July 2011 10:32:07
> *Subject:* Re: [gmx-users] Re: local pressure v4.5 issues
>
> 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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