On Thu, Jul 28, 2011 at 12:05 AM, Jianguo Li <ljg...@yahoo.com.sg
<mailto:ljg...@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.a...@gmail.com <mailto:kgp.a...@gmail.com>>
*To:* Jianguo Li <ljg...@yahoo.com.sg <mailto:ljg...@yahoo.com.sg>>
*Cc:* Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@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 <ljg...@yahoo.com.sg
<mailto:ljg...@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.a...@gmail.com
<mailto:kgp.a...@gmail.com>>
*To:* Jianguo Li <ljg...@yahoo.com.sg <mailto:ljg...@yahoo.com.sg>>
*Cc:* Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@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 <ljg...@yahoo.com.sg
<mailto:ljg...@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.a...@gmail.com
<mailto:kgp.a...@gmail.com>>
*To:* Jianguo Li <ljg...@yahoo.com.sg
<mailto:ljg...@yahoo.com.sg>>; Discussion list for GROMACS
users <gmx-users@gromacs.org <mailto:gmx-users@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.a...@gmail.com <mailto:kgp.a...@gmail.com>> wrote:
On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li
<ljg...@yahoo.com.sg <mailto:ljg...@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.a...@gmail.com
<mailto:kgp.a...@gmail.com>>
*To:* Discussion list for GROMACS users
<gmx-users@gromacs.org <mailto:gmx-users@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.a...@gmail.com <mailto:kgp.a...@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
