leila karami wrote:
Dear all
I want to do Hydrogen bond analysis for my MD data (protein-dna
interaction).
If anybody know the tutorial regarding that, please let me know.
Any help will highly appreciated!
Start with the manual and g_hbond -h, and come back with a more focused
011013021-Jyotsna wrote:
Dear Mark,
Thank you very much for your suggestions.
In the enzyme I am trying to simulate , I need to add 100 H2 molecules
(H2+dummy).
when I tried adding H2 through genion , i came to know genion supports
only monoatomic molecules.
My aim is to replace 100 water
Justin A. Lemkul skrev:
leila karami wrote:
Dear all
I want to do Hydrogen bond analysis for my MD data (protein-dna
interaction).
If anybody know the tutorial regarding that, please let me know.
Any help will highly appreciated!
Start with the manual and g_hbond -h, and come back
I think Justin meant genbox -ci
Tom
Justin A. Lemkul wrote:
011013021-Jyotsna wrote:
Dear Mark,
Thank you very much for your suggestions.
In the enzyme I am trying to simulate , I need to add 100 H2 molecules
(H2+dummy).
when I tried adding H2 through genion , i came to know genion
Thomas Piggot wrote:
I think Justin meant genbox -ci
Indeed, that is correct! Thanks for pointing that out. I know I shouldn't
reply in the morning before I am thoroughly caffeinated...
-Justin
Tom
Justin A. Lemkul wrote:
011013021-Jyotsna wrote:
Dear Mark,
Thank you very much
Please remove my email.
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Hi all,
How do i obtain the protein van der waals and electrostatic energies with
bilayer via residue?
highly appreciate!!
Afsaneh
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mon...@lncc.br wrote:
Please remove my email.
Per the footer of the message you just sent:
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
-Justin
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Ph.D.
afsaneh maleki wrote:
Hi all,
How do i obtain the protein van der waals and electrostatic energies
with bilayer via residue?
Set the appropriate energygrps in the .mdp file and use mdrun -rerun. Note that
if you specify lots of groups you will have that number, squared, written to
On Feb 2, 2010, at 2:24 PM, Matteus Lindgren wrote:
Ok thanks, sounds interesting but I think I need some more details
about how
to run with L-J and Buckingham at the same time even though I have
read the
manual.
You want to use LJ for some pairs and Buckingham for others ? or the two
Dear gmx-users,
I am new to GROMACS. Can anyone tell me what does the last line in .gro file
stands for ?
The manual mentions
box[X][X],box[Y][Y],box[Z][Z],
box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]
Can anyone explain what each of these mean in terms of cell parameters ?
We have mdrun integrated into our distributed computing project. When
your users suspend or close the manger it checkpoints, so when they
open again it continues mdrun where it left off. However, when users
reboot, it starts from the beginning. We are using this command line
to execute the work.
David van der Spoel ha scritto:
On 2/1/10 4:32 PM, ms wrote:
Hi,
Sorry for the offtopic but Google/literature quick search is not helping
and I'd like to have some more informed opinion.
To my understanding, GROMACS isn't capable of discontinuous molecular
dynamics. Is there any
Dear Justin,
Thanks for replying. The table mentions only a few unit cell type. I am
using a monclinic unit cell. Do you know how these box vectors have been
derived.
thanks
vishal
On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Vishal Agarwal wrote:
Dear
Vishal Agarwal wrote:
Dear Justin,
Thanks for replying. The table mentions only a few unit cell type. I am
using a monclinic unit cell. Do you know how these box vectors have been
derived.
Are you talking about your unit cell type, or the structure of the species you
wish to simulate?
Dear Justin,
I am trying to set up calculations for a cellulose structure. The allomorph
of cellulose which I want to study has a monoclinic structure. I have a .cif
file of the XRD structure. I think the better question to ask is how can I
make input files using that.
thanks
vishal
On Tue, Feb
Vishal Agarwal wrote:
Dear Justin,
I am trying to set up calculations for a cellulose structure. The
allomorph of cellulose which I want to study has a monoclinic structure.
I have a .cif file of the XRD structure. I think the better question to
ask is how can I make input files using
Dear list
I recently came up with a problem concerning a replica exchange simulation. The
simulation is run
with gromacs-mpi in Version 4.0.7 compiled with following flags
--enable-threads --enable-mpi --with-fft=mkl -enable-double,
intel compiler version 11.0
mvapich version 1.1.0
mkl version
Hi,
One issue could be MPI memory usage.
I have noticed that many MPI implementations use an amount of memory
per process that is quadratic (!) in the number of processes involved.
This can quickly get out of hand. But 28 GB is a lot of memory.
One thing that might help slightly is to not use
Dear list
I recently came up with a problem concerning a replica exchange simulation. The simulation is run
with gromacs-mpi in Version 4.0.7 compiled with following flags
--enable-threads --enable-mpi --with-fft=mkl -enable-double,
intel compiler version 11.0
mvapich version 1.1.0
mkl
Dear Justin,
Thanks for replying. You mentioned that gromacs supports triclinic
structure. Can you tell me what will be the box parameters for triclinic
structure of cell parameters a, b, c and angles alpha, beta and gama.
Thanks in advance
Vishal
On Tue, Feb 2, 2010 at 12:30 PM, Justin A.
Hi,
Since any unit cell can be formulated as a triclinic cell, the
monoclinic cell is indeed supported. By definition it has two 90 degree
angles and one that is not 90 degrees. The box vectors can be of
different lengths. You'll have to do the math and reading yourself to
find out how this
Hi Vishal,
Here is a python function that generates a triclinic representation
given a definition with lengths and angles. The argument L is a tuple
or list containing the lengths and angles.
def triclinic(L):
B = [[0,0,0],[0,0,0],[0,0,0]]
x, y, z, a, b, c = L[:6]
B[0][0] = x
On 2/2/10 4:43 PM, ms wrote:
David van der Spoel ha scritto:
On 2/1/10 4:32 PM, ms wrote:
Hi,
Sorry for the offtopic but Google/literature quick search is not helping
and I'd like to have some more informed opinion.
To my understanding, GROMACS isn't capable of discontinuous
David van der Spoel ha scritto:
On 2/2/10 4:43 PM, ms wrote:
David van der Spoel ha scritto:
On 2/1/10 4:32 PM, ms wrote:
Hi,
Sorry for the offtopic but Google/literature quick search is not
helping
and I'd like to have some more informed opinion.
To my understanding, GROMACS
- Original Message -
From: Jack Shultz j...@drugdiscoveryathome.com
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS users gmx-users@gromacs.org, Andrey Voronkov
a...@drugdiscoveryathome.com
We have mdrun integrated into our
Hi everyone,
I tried to use mdrun to get the .mtx file, but it does not work, I mean...no
mtx file output.
Below is the command I used in the scripts of my last two trial.
1)
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
## program to run
mpirun -np $NCPUS mdrun_mpi -mtx em.mtx -deffnm em
2)
##
#ZHAO LINA# wrote:
Hi everyone,
I tried to use mdrun to get the .mtx file, but it does not work, I mean...no
mtx file output.
Below is the command I used in the scripts of my last two trial.
1)
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
## program to run
mpirun -np $NCPUS mdrun_mpi -mtx
Hello,
I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620) of
my box of dimensions 3.2418 X 3.2418 X 3.2418 nm. The box is also full of
253 THF molecules. I added the following to the bottom of my .itp file:
#ifdef POSRES
#include posre_Na+.itp
#endif
I wrote the
Jennifer Casey wrote:
Hello,
I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620)
of my box of dimensions 3.2418 X 3.2418 X 3.2418 nm. The box is also
full of 253 THF molecules. I added the following to the bottom of my
.itp file:
#ifdef POSRES
#include
Jennifer Casey wrote:
Thank you so much for your quick response.
I have attached my .itp, and .top files. I think that the if statement
was originally in the wrong spot, but after changing in and running an
energy minimization, there is still some drifting - the Na+ moves to
(0.566,
Hi Tsjerk,
Thanks for replying. I was going through the pdb format dcoument on the PDB
webpage. I found that the box corresponds to the following:
a b(cos(gama)) c(cos(beta))
0 b(sin(gama)) c(cos(alpha) - cos(beta) cos(gama) / sin(gama)
00 V/(ab sin(gama))
where V
Hi,
I just simply did a change in .mdp file. Now the integrator = nm
after grompp,
1) below is the error of mdrun -s em.tpr -mtx em.mtx
Program mdrun, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/smalloc.c, line: 147
Fatal error:
Not enough memory. Failed to calloc
#ZHAO LINA# wrote:
Hi,
I just simply did a change in .mdp file. Now the integrator = nm
after grompp,
1) below is the error of mdrun -s em.tpr -mtx em.mtx
Program mdrun, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/smalloc.c, line: 147
Fatal error:
Not enough memory.
I will try it without the checkpointing flags. If that fails, maybe
I'll introduce some python into this integration. Check if the
checkpoint already exists.
On Tue, Feb 2, 2010 at 6:18 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
- Original Message -
From: Jack Shultz
Dear gromas users,
I am new to gromacs and trying to run polyacrylate MD simulation. I obtained
an itp file using PRODRG (gromos 96 force-field parameters). When I compare
with the same forcefield parameters in the gromacs/top directory, they are
far too off. For eg.
[ bonds ]
; ai aj fu
On 03/02/10 15:44, Jack Shultz wrote:
I will try it without the checkpointing flags.
That's not quite what I said. I suggested not using *different*
filenames for -cpo and -cpi. What you want is the output file from a
former run to transparently become the input file for the subsequent
one,
So you mean something like -cpi state.cpt -cpo state.cpt ? If so, I'll
try this approach again. I had a little trouble doing it this way
previously. I think I had trouble with the extension scripts doing it
this way.
On Tue, Feb 2, 2010 at 11:56 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On
On 03/02/10 16:38, Jack Shultz wrote:
So you mean something like -cpi state.cpt -cpo state.cpt ? If so, I'll
try this approach again. I had a little trouble doing it this way
previously. I think I had trouble with the extension scripts doing it
this way.
I'd equilibrate, then use mdrun -cpi
On 03/02/10 15:55, sulatha M. S wrote:
Dear gromas users,
I am new to gromacs and trying to run polyacrylate MD simulation. I
obtained an itp file using PRODRG (gromos 96 force-field parameters).
When I compare with the same forcefield parameters in the gromacs/top
directory, they are far too
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