On Fri, Aug 30, 2013 at 11:18 AM, Venkat Reddy venkat...@gmail.com wrote:
Dear Gromacs users,
I am analyzing the density of my spherical lipid vesicle using g_densmap
tool with the following options.
g_densmap -f vesicle_noPBC.xtc -s vesicle-12us.tpr -n index.ndx -dt 1000
-od -amax 6
Nitin,
You can use g_polystat and see if you can reproduce your observations.
Chandan
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Dear gmx users,
I have calculated the bonded distibutions of a polymer melt by writing an
analysis tool (template.c). The tool was written in gmx 4.0.7 version.
code snippet
* do {
/* coordinates are
There are no such directory.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Jun 12, 2013 at 1:56 PM, colinbannister
colin.bannis...@nottingham.ac.uk wrote:
Hope I'm not missing something obvious here - but I can't find the
'share/tutor' directory in my Gromacs 4.6
I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7).
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
They're still fine. There must be a problem at your end, I'm afraid.
Mark
On Sat, Jun 8, 2013 at
Hi Albert,
I think using -nt flag (-nt=16) with mdrun would solve your problem.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Tue, Jun 4, 2013 at 12:56 PM, Albert mailmd2...@gmail.com wrote:
Dear:
I've got four GPU in one workstation. I am trying to run two GPU job with
Dear gmx users,
I had installed gromacs 4.6.1 using cmake. All the binaries are installed,
but surprisingly I do not find ngmx executable. Can anyone guide me how do
I install ngmx using cmake.
Chandan
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NCL, Pune
INDIA
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gmx-users mailing listgmx-users@gromacs.org
. Vitaly Chaban
On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury iitd...@gmail.com
wrote:
Dear gmx users,
I had installed gromacs 4.6.1 using cmake. All the binaries are
installed,
but surprisingly I do not find ngmx executable. Can anyone guide me how
do
I install ngmx using cmake
You need to re submit the jobs, with decreased time.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Apr 6, 2013 at 11:20 AM, dina dusti dinadu...@yahoo.com wrote:
Dear Specialists
I am a beginner at Gromacs. I work with MARTINI CG force field.
I selected 5 for
nstxout=
On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote:
Hi,
The code compiled, so the compiler is not the issue.
I guess mdrun picked up GPU 0, which it should have ignored. You only want
to use GPU 1.
Could you try running:
mdrun -ntmpi 1 -gpu_id 1
$mdrun_461 -ntmpi 1
On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll szilard.p...@cbr.su.sewrote:
Hi,
If mdrun says that it could not detect GPUs it simply means that the GPU
enumeration found no GPUs, otherwise it would have printed what was found.
This is rather strange because mdrun uses the same mechanism the
Hi !!
I problem with the permission of /dev/nvidia*
changed it to 0666 /dev/nvidia*
Everything resolved. mdrun can be executed as normal user.
Thanks everyone.
Chandan
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Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Mar 28, 2013 at 4:26 PM, Chandan Choudhury iitd...@gmail.comwrote
Dear GMX Users,
I am trying to execute Gromacs 4.6.1 on one of the GPU server:
*OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release)
*gcc*: 4.7.2
CUDA Library paths
#CUDA-5.0
export CUDA_HOME=/usr/local/cuda-5.0
export PATH=$CUDA_HOME/bin:$PATH
export
Hi Boopathi,
Adding hydrogen atoms to the hdb is explained in the sectio 5.6.4 of
gromacs manual 4.5.4. Please refer the manual.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Jan 10, 2013 at 11:32 AM, Subramaniam Boopathi
boopathi...@gmail.com wrote:
Dear All
On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh shima_arasteh2...@yahoo.com
wrote:
Dear all,
I had a .pdb file containing protein, popc, and ions. So I used editconf
to make a .gro file. But when I want to make an index file, 2 CL ions are
not identified, so I can not choose it.
use
On Mon, Dec 31, 2012 at 1:07 PM, Chandan Choudhury iitd...@gmail.comwrote:
On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh
shima_arasteh2...@yahoo.com wrote:
Dear all,
I had a .pdb file containing protein, popc, and ions. So I used editconf
to make a .gro file. But when I want to make
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner ckut...@gwdg.de wrote:
Hi Chandan,
On Nov 29, 2012, at 3:30 PM, Chandan Choudhury iitd...@gmail.com wrote:
Hi Carsten,
Thanks for your suggestion.
I did try to pass to total number of cores
,
g_tune_pme
checks only up to npme = np/2 PME nodes.
Best,
Carsten
On Dec 4, 2012, at 1:54 PM, Chandan Choudhury iitd...@gmail.com wrote:
Dear Carsten and Florian,
Thanks for you useful suggestions. It did work. I still have a doubt
regarding the execution :
export MPIRUN=`which
On Tue, Dec 4, 2012 at 7:18 PM, Carsten Kutzner ckut...@gwdg.de wrote:
On Dec 4, 2012, at 2:45 PM, Chandan Choudhury iitd...@gmail.com wrote:
Hi Carsten,
Thanks for the reply.
If PME nodes for the g_tune is half of np, then if it exceeds the ppn of
of
a node, how would g_tune
of the cores over the nodes may have
to be specified in a hostfile / machinefile. Check g_tune_pme -h
on how to set that.
Best,
Carsten
On Aug 28, 2012, at 8:33 PM, Chandan Choudhury iitd...@gmail.com wrote:
Dear gmx users,
I am using 4.5.5 of gromacs.
I was trying to use g_tune_pme
Dear Rajiv,
Please start a different thread, if you want to get help. I suppose
you need to be informative regarding your error(s).
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Oct 19, 2012 at 2:07 PM, Rajiv Gandhi graji...@gmail.com wrote:
Dear Gromacs,
I am trying to
Dear gmx users,
I am using 4.5.5 of gromacs.
I was trying to use g_tune_pme for a simulation. I intend to execute
mdrun at multiple nodes with 12 cores each. Therefore, I would like to
optimize the number of pme nodes. I could execute g_tune_pme -np 12
md.tpr. But this will only find the optimal
Dear gmx users,
I am using 4.5.5 of gromacs.
I was trying to use g_tune_pme for a simulation. I intend to execute
mdrun at multiple nodes with 12 cores each. Therefore, I would like to
optimize the number of pme nodes. I could execute g_tune_pme -np 12
md.tpr. But this will only find the optimal
On Fri, Aug 17, 2012 at 2:16 PM, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
After a production MD, both the xtc file and trr file are produced. trr
file is much larger than the xtc file. But when we openned the original gro
file one of the file from xtc file and trr file in VMD, we
Nidhi,
To get reply from the gmx community, you need to post the error messages
which erupts while compiling.
Chandan
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Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Jun 18, 2012 at 11:43 AM, Nidhi Jatana nidhijat...@bic-svc.ac.inwrote:
Dear Sir/Madam
Thanks for all the help. I have
Ok.
You need to source the GMXRC file
Follow http://www.gromacs.org/Documentation/Installation_Instructions
For bash shell: if your executables are in /usr/local/gromacs/bin
$source /usr/local/gromacs/bin/GMXRC
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Jun 18, 2012 at 11:54
Dear gmx users,
Is it possible to redirect the output of mdrun -v to a file while
submitting the job using pbs script?
mdrun -v -s md.tpr verbose.txt
donot produce output (to file verbose.txt) while the job is running.
Chandan
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NCL, Pune
INDIA
--
gmx-users mailing
output (from both stdout and
stderr) you should use:
mdrun -v -s md.tpr verbose.txt
Thanks. It is actually mdrun -v -s md.tpr verbose.txt
Javier
El 18/06/12 08:49, Chandan Choudhury escribió:
Dear gmx users,
Is it possible to redirect the output of mdrun -v to a file while
and stderr output through the -o and -e parameters,
respectively.
On 2012-06-18 05:28:11PM +0530, Chandan Choudhury wrote:
On Mon, Jun 18, 2012 at 12:43 PM, Javier Cerezo j...@um.es wrote:
Information messages, such as those shown on the screen during mdrun
are
output to stderr. So
trjconv -dt
use dt flag with the utility trjconv
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Jun 15, 2012 at 12:07 PM, a a pat...@hotmail.com wrote:
try ptraj
--
Date: Fri, 15 Jun 2012 10:18:40 +0400
Subject: Re: [gmx-users] analysing of the
Use editconf http://manual.gromacs.org/current/online/editconf.html
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sun, Jun 10, 2012 at 11:30 PM, Matthias Ernst
matthias.ern...@student.kit.edu wrote:
Why do you want to use Gromacs?
I would suggest to use openBabel, which can convert
On Thu, May 24, 2012 at 10:39 AM, Seera Suryanarayana
paluso...@gmail.comwrote:
Dear all gromacs users,
I am new for MD and in particular using
gromacs software.I would like to learn basics of gromacs.Please tell me the
name of the manual which one is
On Sat, Feb 25, 2012 at 12:09 PM, priya thiyagarajan
priya.thiyagaraja...@gmail.com wrote:
hello sir,
i was performing simulation for 30ns.
due to queue time limit my mdrun stopped at 11.6ns.. then i extended my
simulation using these two commands
*tpbconv -s md.tpr -extend 2 -o
I correct?
But if you remove jumps first, you're fine anyway. Just don't put
things back in the box afterwards. And don't center if your aim is
calculating MSDs.
Yeah, you are right.
Chandan
Hope it helps,
Tsjerk
On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury iitd...@gmail.com
Dear gmx-users,
I have a simulated a system containing a linear polymer in a cubic box with
water molecules. I need to get rid of PBC effect on the system such that I
can execute my own analysis code. I intend to compute the msd of water
molecules along the polymer backbone. So, when I execute
On Thu, Dec 8, 2011 at 12:33 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 8/12/2011 2:54 PM, Chandan Choudhury wrote:
Thanks everyone for the responses. I should have framed my question much
more precisely. I am trying to use the template.c code of (gmx_4.0.7) and
within this, I want
Dear gmx_users,
I am using gmx_4.0.7. I need to print the box vectors from the trajectory
of a simulated system. How can this be achieved? Can someone help me out?
Chandan
--
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NCL, Pune
INDIA
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gmx-users mailing listgmx-users@gromacs.org
Dear gmx_users,
I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the
PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer
and at some point of the trajectory, some lipid molecules, due to PBC in
the lateral direction, might pop out from one side of the
that the g_energy prints the box vector with the simulation
time. But, trjconv -dump also writes the box vectors in the pdb file.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Dec 8, 2011 at 3:33 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 8/12/2011 4:36 AM, Chandan Choudhury wrote
For any text file, use your favorite editor to delete all your water
molecules. It will load very fast. For the xtc/trr files, use trjconv with
an index file to write a new xtc/trr file without water molecules. Index
file should contain the atom nos. of the molecules you want.
trjconv -s a.tpr -f
Hi gmx-users,
Is it possible to extend a simulation with change in the output control
parameter (nstxtcout)?
I am aware of that tpbconv can extend a simulation with the same output
controls as in the input tpr file.
Chandan
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NCL, Pune
INDIA
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gmx-users mailing list
Dear gmx users,
A simulation was performed for 50 ns with
; RUN CONTROL
integrator = md
nsteps = 5000
dt = 0.001
; OUTPUT CONTROL
nstxout = 1000
nstvout = 1000
nstxtcout= 0
nstlog
On Fri, Oct 21, 2011 at 10:26 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 21/10/2011 3:25 PM, Chandan Choudhury wrote:
Dear gmx users,
A simulation was performed for 50 ns with
; RUN CONTROL
integrator = md
nsteps = 5000
dt
22, 2011 at 1:53 PM, Chandan Choudhury iitd...@gmail.com
wrote:
Hi gmx-users,
I was trying to feed make_ndx with the non-interactive script, below
is my command:
The script called choice.txt contained:
ri 1-20
ri 21-40
ri 41-60
ri 61-80
ri 81-100
ri 101-120
Initially, I used
Carla,
The g_residence.c is written in accord to gmx-4.5.4 format. What you
can do is copy it to the src/tools directory. Make a subsequent
changes in the Makefile present there and the do make to compile. This
will generate g_residence executable, which can be used.
But I did not understand,
Hi gmx-users,
I was trying to feed make_ndx with the non-interactive script, below
is my command:
The script called choice.txt contained:
ri 1-20
ri 21-40
ri 41-60
ri 61-80
ri 81-100
ri 101-120
Initially, I used the bash shell, then csh and tcsh, but in both the
cases it failed to produce the
Hi gmx-users,
I tried installing the tool, g_residence.c
I am using gromacs-4.0.7
I copied it to the src/tools. There, I executed make command
# make g_residence
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -I/opt/fftw-3.2.2/include -L/opt/fftw-3.2.2/lib
message already shows some hints. Try recompile FFTW with
-fPIC.
Jianguo
__
From: Chandan Choudhury iitd...@gmail.com
To: gmx-users gmx-users@gromacs.org
Sent: Thursday, 2 June 2011 15:03:03
Subject: [gmx-users
Hello gmx-users,
I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64.
1. I installed fftw 3.2.2
./configure --prefix /soft/sudip/abc/execs/fftw/
--enable-single --enable-threads
2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file
a)
Hello gmx-users !!
I tried using g_hbond tool to analyse h-bonds on my system. I could
successfully execute the tool for two of my systems. But the third system
should the memory problem. Below I have pasted my command and its output.
*$ g_hbond -s ../md0-20.tpr -f 40-50.trr -n index_2.ndx -num
I missed my Gromacs version. It's 4.0.7
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Wed, Apr 13, 2011 at 4:58 PM, Chandan Choudhury iitd...@gmail.comwrote:
Hello gmx-users !!
I tried using g_hbond tool to analyse h-bonds on my system. I could
successfully execute the tool for two of my
Hi all !!
Can some one clarify me what the g_mindist does. As far as I understood, it
takes two inputs from the index file. If I have more than one entry in both
of the indexes than how would g_mindist function?
eg; echo 7 8 | g_mindist -s ../md30-60.tpr -n index.ndx -f
../30-60.part0004.trr
Hello all !!
I have a 30 ns trajectory in two parts (0-20 20-30). I am using Gromacs
4.0.7. I concatenated using trjcat (*echo 2 | trjconv -s md10-30.tpr -f
0-30.trr -o pbc_whole.trr -n index_grdf.ndx -nice 0*).
Then I converted the concatenated trajectory into pbc trajectory using
trjconv
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Dec 24, 2010 at 3:13 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 24/12/2010 4:58 AM, Chandan Choudhury wrote:
Hello all !!
I have a 30 ns trajectory in two parts (0-20 20-30). I am using Gromacs
4.0.7. I concatenated using trjcat
Hi Vinoth !!
Try genbox with increasing the vander Waal's radii.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Oct 4, 2010 at 5:03 PM, vinothkumar mohanakrishnan
kmvin...@gmail.com wrote:
hi Mark
After deleting half the molecules of decane from the box and if i use
genbox
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul jalem...@vt.edu wrote:
abdullah ahmed wrote:
Hello,
I'd like to ask a question about the conversion of the results of
minimization to pdb format. Here is what I do:
1. Apply pdb2gmx to the
Hello gmx users !!
I was trying to use template.c. There I printed out the coordinates of a
trajectory file using the printf statement as under:
printf(Coordinates at t=%8.3f : %8.5f %8.5f
%8.5f\n,fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]);
The output was
Reading frame 100 time 4400.000
The suggestions were very helpful.
Thanks
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sun, May 30, 2010 at 11:32 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi Chandan,
The problem is that with floating points the equality in
if (fr.time == (4000.000 + (50.0 * inc)))
is
Hello all !!
I was playing around with template.c and stuck in a problem.
In the program inside the do loop i.e;
/* This is the main loop over frames */
do {
/* coordinates are available in the vector fr.x
* you can find this and all other structures in
* the types directory
Have a loolk at
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
Chadnan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, May 13, 2010 at 10:34 AM, manjula kasinathan manju...@gmail.comwrote:
Hi all
i have done protein protein interaction and the
Hi gmx users !!
I want to read the trajectory file (*.trr ), produced as a result of mdrun.
I came to know that a file template.c already exists to facilate my process.
I could compile and execute the template.c. Like
printf(Atom name: %s\n,*(top.atoms.atomname[n]));
printf(Atom charge:
Thanks Justin. It worked perfectly.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Tue, Apr 13, 2010 at 1:08 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Chandan Choudhury wrote:
Hello gmx-users
I am trying to simulate an amino acid (say GLN). It can be as a
zwitterionic form
Hello gmx-users
I am trying to simulate an amino acid (say GLN). It can be as a zwitterionic
form or uncharged ends. Neither ffamber or ffopls force fields has a
complete parameter for them. While in ffamber, I have the parameters for
CGLU and NGLU, but not for a Glutamine. Do I need to define it
Hello gmxusers !!!
I want to continue my simulation, from where the point where it stopped. The
gmxcheck on .trr and cpt files are as:
$gmxcheck -f state.cpt
Checking file state.cpt
# Atoms 186864
Last frame -1 time 9362.500
Item#frames Timestep (ps)
Step 1
Time
where the cpt file was
written.
Any suggestions??
chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 17/02/10 02:52, Chandan Choudhury wrote:
Hello gmxusers !!!
I want to continue my simulation, from where
0
Box 1
Here also the time is greater than the .trr file.
Cant understand how to overcome it.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Tue, Feb 16, 2010 at 11:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Chandan Choudhury wrote:
Hi Mark !!!
Thanks
16, 2010 at 11:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 17/02/10 04:43, Chandan Choudhury wrote:
Thanks Justin !!
But my state_prev.cpt file shows
$gmxcheck -f state_prev.cpt
Checking file state_prev.cpt
# Atoms 186864
Last frame -1 time 9346.700
Item
instead of the state_prev.cpt file in order
to avoid losing time.
Hope this helps.
Lum
On 17/02/10 02:52, Chandan Choudhury wrote:
Hello gmxusers !!!
I want to continue my simulation, from where the point where it stopped.
The gmxcheck on .trr and cpt files are as:
$gmxcheck -f
:
On 13/02/10 15:29, Chandan Choudhury wrote:
What is a cross-compiler?
One that compiles an executable for architecture other than the one on
which compilation occurs.
My system is
x86_64 x86_64 x86_64 GNU/Linux
model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz
vendor id
Hello gmx users !!
I installed successfully installed fftw. Then tried compiling gmx parallely
I executed the command
$ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/
It didnot show any problem.
$make
make[5]: Entering directory
/10, *Chandan Choudhury * iitd...@gmail.com wrote:
Hello gmx users !!
I installed successfully installed fftw. Then tried compiling gmx parallely
I executed the command
$ ./configure --enable-mpi --prefix=/home/vanka/NUM-GEN/GRO/
It didnot show any problem.
$make
make[5]: Entering
Thanks berk.
By the way, if I dont give -p topol.top as input to genion, then genion
executes. In this case, I manually edit the topology file and add the ion
information.
[ molecules ]
; Compound#mols
Protein_A 1
Protein_B 1
Protein_C 1
Protein_D 1
Hello gmxusers !!
I am simulating a protein and it is bound to ATP.
Simulation of protein alone (without) works fine. Solely ATP simulation too
works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb)
file.
Error:
$ genion -s em.tpr -o ion.pdb -p topol.top -np 48
WARNING:
, trr and edr files. What I found here was the .trr
(generated using cpi flag) file had all the frames.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 8, 2010 at 5:21 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Chandan Choudhury wrote:
Hello gmxusers !!
gmxcheck
at one of the entries from the ffamberXX.rtp file and
work out how this is used by pdb2gmx it should become clear what you need to
do to add the ATP to the forcefield.
Cheers
Tom
--On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury
iitd...@gmail.com wrote:
Hi Thomas
As Justin said give the command line options for mdrun and also check that
your mpi environment is running. Better to run a parallel job and check its
output.
Chadnan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 8, 2010 at 8:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
is located suggests that the gamma
phosphate should be protonated then you need to use other ATP parameters
which include this hydrogen (such as those in the GROMOS forcefield).
Cheers
Tom
Chandan Choudhury wrote:
Hi Tom!!
Thanks for the information. I went through the paper and added
I had a simple query regarding the rtp file . What does the '+' and '-' sign
indicates in the following dihedral inforamtion:
[ dihedrals ]
CA C+N+Hbackbone_prop_1
O C+N+Hbackbone_prop_2
-C NCACBbackbone_prop_3
-C NCA C
Hello gmxusers !!
gmxcheck on #spc_25_eq.trr prints: (#spc_25_eq.trr is the renamed from
#spc_25_eq.trr.1#. mdrun was stopped due to insufficient space)
Checking file #spc_25_eq.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 2000.000
# Atoms 33885
Reading frame
I had also had trouble installing gmx (paralley). But now, its solved.
I would suggest you to see that the mpi is running or not.
Here is a sample mpi C program:
#include stdio.h
#include mpi.h
int main( argc, argv )
int argc;
char **argv;
{
Hello gmx users,
I need to use ATP's parameter for amber port in gromacs. The atp.prep and
frcmod.phos for ATP can be found at
http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in
ffamber.
The program amb2gmx.pl needs amber to be installed, which is not present.
Same with ACPYPI.
killed!
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 1, 2010 at 10:50 AM, Sarath Kumar bskumar.t...@gmail.comwrote:
Message: 5
Date: Sun, 31 Jan 2010 00:34:22 +0530
From: Chandan Choudhury iitd...@gmail.com
Subject: Re: [gmx-users] error: Cannot compile and link MPI code
Hi gmx users !!
On compiling GMX paralley, following error was encountered. How can I tackle
this.
Kindly help.
checking for mpicc... mpicc
checking whether the MPI cc command works... configure: error: Cannot
compile and link MPI code with mpicc
The config.log file reads
configure:4536:
Choudhury
NCL, Pune
INDIA
On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz rol...@utk.edu wrote:
Hi,
your MPI installation has to be brogen. mpicc always has to be able to find
libmpi. Please reinstall mpi correctly.
Roland
On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury iitd
I am using openmpi-1.4.1.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sun, Jan 31, 2010 at 12:34 AM, Chandan Choudhury iitd...@gmail.comwrote:
Hi Ronald !!
Thanks for your reply.
I recompiled the openmpi. But while executing ./configure --enable-mpi in
gromacs4.0.7 the following error
Hi Tom !!!
Can you guide to incorporate the AMBER parameter for ATP (
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof) in ffamber. I am using
ffamber for the simulation of Protein + ATP.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Jan 21, 2010 at 7:06 PM, Thomas Piggot
the solution was:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/your/directory/openmpi/lib
of course you have to change /your/directory with the correct path in
your system.
I hope this will help.
Nuno Azoia
On Fri, 2010-01-15 at 12:30 +0530, Chandan Choudhury wrote:
Hello gmx-users !!
I am
Hello gmx-users !!
I am trying to install gromacs 4.0.7 double precision with mpi. I downloaded
openmpi-1.4. and installed it.
Then executed
./configure --enable-mpi --program-suffix=_mpi_d
--prefix=/usr/local/gromacs407_double_mpi --enable-double
It showed checking for mpicc...
mpicc
checking
Nilesh
The atom type C is for Carbon and for chlorine is Cl. So, substitute
Chlorine's atom type with Cl.
Chandan
On Tue, Nov 17, 2009 at 9:04 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote:
Hello,
My system is having chlorin atoms. Duing pdb2gmx it treat Chlorne atoms as
carbon.
Can you
Hi everyone !!
I am having a problem using pdb2gmx command. Using the command on my input
pdb file, it results saying Fatal error: Atom O in residue CCMT 1 not found
in rtp entry with 38 atoms while sorting atoms. I do not have only O
either in input pdb file or in rtp file. and its O and not 0
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