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

Thu Jul 28 17:59:18 CEST 2011

I just checked that the mdrun of v4.0.2_local_pressure can read the tpr
generated from grompp of v4.0.7. I did get some local pressure numbers. Also
i checked the potential energy between 4.0.2 and 4.0.7 there is a difference
of about 0.0008% .

I am just wondering how this problem got fixed ie how could 4.0.2 did not
have trouble reading the tpr of 4.0.7 whereas 4.0.2 could not make the tpr
file (it complains about Invalid dihedral type 9).

On Thu, Jul 28, 2011 at 12:05 AM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:

> Use grompp of v4.0.7 to generate the tpr files using CHARMM FF and give
> this tpr file to v4.0.2_local_pressure to rerun the simulation.
>
> 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:* Thursday, 28 July 2011 09:27:04
>
> *Subject:* Re: [gmx-users] Re: local pressure v4.5 issues
>
> 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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