[gmx-users] Re: local pressure v4.5 issues
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 28 18:04:48 CEST 2011
Amit Choubey wrote:
> 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).
>
New features get implemented. In this case, type 9 dihedrals were added after
version 4.0.2, so grompp didn't know how to handle them. Minor versions (i.e.
4.0.x) generally have compatible file types. So grompp version 4.0.7 compiled a
.tpr file that mdrun 4.0.2 could handle since the file format was the same, but
the information therein was different. Note that this applies only to *minor*
version differences, e.g. 4.5 .tpr files cannot be read by 4.0.x mdrun.
-Justin
> On Thu, Jul 28, 2011 at 12:05 AM, Jianguo Li <ljggmx at yahoo.com.sg
> <mailto: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 <mailto:kgp.amit at gmail.com>>
> *To:* Jianguo Li <ljggmx at yahoo.com.sg <mailto:ljggmx at yahoo.com.sg>>
> *Cc:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto: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
> <mailto: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
> <mailto:kgp.amit at gmail.com>>
> *To:* Jianguo Li <ljggmx at yahoo.com.sg <mailto:ljggmx at yahoo.com.sg>>
> *Cc:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto: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
> <mailto: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
> <mailto:kgp.amit at gmail.com>>
> *To:* Jianguo Li <ljggmx at yahoo.com.sg
> <mailto:ljggmx at yahoo.com.sg>>; Discussion list for GROMACS
> users <gmx-users at gromacs.org <mailto: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 <mailto:kgp.amit at gmail.com>> wrote:
>
>
>
> On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li
> <ljggmx at yahoo.com.sg <mailto: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
> <mailto:kgp.amit at gmail.com>>
> *To:* Discussion list for GROMACS users
> <gmx-users at gromacs.org <mailto: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 <mailto: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
>
>
>
>
>
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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