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

[Amit Choubey]

Hi all,

I am trying to figure out a way to port tpr files (which has CHARMM FF) from
v4.5 to v4.0.2. This is because i want to use the localpressure calculation
which works only in version 4.0.2.

When i issue the following command i get

grompp_v4.0.2_lp -v -c traj0.gro -o npt_4.0 -p system.top -f rerun.mdp

I get the following error
*
*

Program grompp_v4.0.2_lp, VERSION 4.0.2_localpressure

Source code file: topdirs.c, line: 118



Fatal error:

Invalid dihedral type 9

I think dihedral type 9 is not defined until version 4.0.7. Could anyone
provide a way to deal with this ?

Amit

On Thu, Jun 30, 2011 at 9:39 PM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:

> I downloaded v4.5 and v4.0 from the same websites as you mentioned in
> previous email. I am not sure why v4.5 give inconsistent results. I haven't
> try v4.0, because my simulation is using CHARMM FF. Could you give more
> details of conversion tpr files from v4.5 to v4.0 using CHARMM FF?
>
> Thank you very much!
>
> Cheers,
> Jianguo
>
>
>
> ------------------------------
> *From:* Amit Choubey <kgp.amit at gmail.com>
> *To:* Jianguo Li <ljggmx at yahoo.com.sg>
> *Cc:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Friday, 1 July 2011 11:47:58
>
> *Subject:* Re: [gmx-users] Re: local pressure v4.5 issues
>
>
>
> 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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