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

Thu Jul 28 09:08:12 CEST 2011

I have tried CHARMM FF in v4.0.4 and it does not give error, so it seems 
dihedral type 9 has already been implemented in v4.0.4.
Jianguo

________________________________
From: Jianguo Li <ljggmx at yahoo.com.sg>
To: Amit Choubey <kgp.amit at gmail.com>
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, 28 July 2011 15:05:19
Subject: Re: [gmx-users] Re: local pressure v4.5 issues

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 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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