Hi,
With the Mark Abraham's scripts and advices, I have finally resolved my
problems.
Thank you and see ya on the list
Stéphane
Message d'origine
De: gmx-users-boun...@gromacs.org de la part de gmx-users-requ...@gromacs.org
Date: lun. 01/02/2010 17:27
À: gmx-users@gromac
Justin A. Lemkul wrote:
Julian Garrec wrote:
Dear GROMACS users,
I am trying to equilibrate my system (monomeric protein in water) and I
want to use position restraint on heavy atoms of the solute using the
posre.itp file. For some reason, grompp applies correctly the force
constant I wan
Hi,
I wasn't fast enough answering this but I sent you an e-mail off-list. And as I
said, when you get this to work you can put this on the Downloads->User
contributions->Force fields on gromacs.org.
Regards,
Pär Bjelkmar
> Hi,
>
> With the Mark Abraham's scripts and advices, I have finally
Hi,
Is it possible to use both Lennard-Jones and Buckingham parameters in the
same simulation?
If not, can the program sigeps convert from Buckingham to LJ? It seems to me
it cannot.
Thanks
Matteus
-
Matteus Lindgren, graduate
On Feb 2, 2010, at 11:25 AM, Matteus Lindgren wrote:
Hi,
Is it possible to use both Lennard-Jones and Buckingham parameters
in the same simulation?
I believe it does allow it, you need to define the potentials and give
the corresponding one to the
atom pairs concerned.
See the chapter on
Julian Garrec wrote:
Justin A. Lemkul wrote:
Julian Garrec wrote:
Dear GROMACS users,
I am trying to equilibrate my system (monomeric protein in water) and
I want to use position restraint on heavy atoms of the solute using
the posre.itp file. For some reason, grompp applies correctly th
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 molecules randomly by H2.
How
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
question
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 mo
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 with
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 supports
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 fo
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.
On a side note, it seems sigeps can only convert from L-J to Buckingham not
the other way around. In addition, the fit of the two potent
Please remove my email.
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Please search the archive at http://www.gromacs.org/search before posting!
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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
--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/searc
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
--
Justin A. Lemkul
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
toge
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 ?
Tha
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.
m
Vishal Agarwal wrote:
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 ter
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
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 wrote:
>
>
> Vishal Agarwal wrote:
>
>> Dear gmx-users,
>>
>> I
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 that.
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 do
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
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. Lemku
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
i
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 molecul
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.
>>
- Original Message -
From: Berk Hess
Date: Wednesday, February 3, 2010 5:13
Subject: RE: [gmx-users] Replica Exchange MD on more than 64 processors
To: Discussion list for GROMACS users
---
|
>
Hi,
>
> One issue could be M
- Original Message -
From: Jack Shultz
Date: Wednesday, February 3, 2010 2:36
Subject: [gmx-users] Checkpointing
To: Discussion list for GROMACS users , Andrey Voronkov
> We have mdrun integrated into our distributed computing project. When
> your users suspend or close the manger it
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 em.
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 posre_N
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 "posre_Na+.it
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, 1.559,
1.586) from (0.486, 1.621, 1
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, 1.559,
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 411894404
#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. Fa
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 wrote:
>
>
> - Original Message -
> From: Jack Shultz
> Date: Wednesday, February 3,
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 fuc0
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 wrote:
> On 03/02/10 15:44, Jack S
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 st
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 off
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