When calculated during the md run, the corresponding options in g_energy
for the dipole moment are MU-X, MU-Y and MU-Z.
However, taking into account the previous mail by David van der Spoel,
it's possible that the dipole moment could not be calculated in your
system. Options in g_energy vary
Dear Gromacs,
I am trying to install gromacs with mpi enabled in my cluster and i end
up with following error:
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error
I can able to install gromacs
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
Hi
The dipole is stored in the edr file, which output frequency is
controlled by nstenergy option in the mdp parameter file. Set it
appropriately during your run (nstenergy=0.003) but keep in mind that it
should be a multiple of the time step.
Javier
El 18/10/12 18:09, Nilesh Dhumal
On 10/18/12 1:45 PM, Javier Cerezo wrote:
Hi
The dipole is stored in the edr file, which output frequency is controlled by
nstenergy option in the mdp parameter file. Set it appropriately during your
run (nstenergy=0.003) but keep in mind that it should be a multiple of the time
step.
On 2012-10-18 18:09, Nilesh Dhumal wrote:
Hello,
I am calculating the dipole moment auto-correlation function for my system
which have 128 cation and 128 anion.
I am saving the trajectory at each 2 ps and using this trajectory for
further analysis.
Can I save the dipole moment and three
In short, I can save dipole moment with the same frequency, the
trajectory save.
Nilesh
On 10/18/12 1:45 PM, Javier Cerezo wrote:
Hi
The dipole is stored in the edr file, which output frequency is
controlled by
nstenergy option in the mdp parameter file. Set it appropriately
during
In short, I can not save dipole moment directly. I can calculate dipole
moment only using .trr file.
Nilesh
On 10/18/12 1:45 PM, Javier Cerezo wrote:
Hi
The dipole is stored in the edr file, which output frequency is
controlled by
nstenergy option in the mdp parameter file. Set it
Justin is right. I've slipped a bit, that was not the way to set
nstenergy. But still, you can save the dipole directly in the edr file.
Not from your existing trajectory, but in a new run. Say your dt=1fs,
then you should set nstenergy=3 to get your dipole moment every 3fs
which you can
How can I save the total dipole moment extacted by .edr file?
I could not find the option in g_energy.
Nilesh
Justin is right. I've slipped a bit, that was not the way to set
nstenergy. But still, you can save the dipole directly in the edr file.
Not from your existing trajectory, but in a
Is it possible to calcualte the dipole moment at 3fs by modifing the
source code?
Nilesh
How can I save the total dipole moment extacted by .edr file?
I could not find the option in g_energy.
Nilesh
Justin is right. I've slipped a bit, that was not the way to set
nstenergy. But still,
On Fri, 2012-05-18 at 09:49 -0700, Milinda Samaraweera wrote:
Hi Guys
Could you please explain to me how to use the g_dipole method to
calculate the dipole moment of a Solute in a solvent.
Hi,
there has just recently been a discussion on this mailing list. Actually
you need just an
.
Best Regards
Dina
From: Justin A. Lemkul jalem...@vt.edu
To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Sunday, May 13, 2012 5:23 PM
Subject: Re: [gmx-users] dipole moment
On 5/13/12 8:41 AM, dina dusti wrote:
Dear GROMACS
From: Justin A. Lemkul jalem...@vt.edu
To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Sunday, May 13, 2012 5:23 PM
Subject: Re: [gmx-users] dipole moment
On 5/13/12 8:41 AM, dina dusti
Subject: Re: [gmx-users] dipole moment
On 5/13/12 8:41 AM, dina dusti wrote:
Dear GROMACS Specialists,
I have one system consists of water and two other molecules. I
work by MARTINI
CG force field. I want to calculate dipole moment of molecules in
water.
May I ask you to help me, Please
From: Justin A. Lemkul jalem...@vt.edu
To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Sunday, May 13, 2012 5:23 PM
Subject: Re: [gmx-users] dipole moment
On 5/13/12 8:41 AM, dina dusti wrote:
Dear GROMACS Specialists,
I have one system consists of water and two other molecules. I work by MARTINI
CG force field. I want to calculate dipole moment of molecules in water.
May I ask you to help me, Please?
I doubt you can. Unless you are using
I want to see the change in dipole moment alond the simulation.
NIlesh
On Wed, May 25, 2011 11:32 am, David van der Spoel wrote:
On 2011-05-25 17.14, Nilesh Dhumal wrote:
Hello,
Can I calculate a dipole moment of a particular bond?
It is easier to do it manually. Otherwise g_dipoles
Thanks for reply.
Here are more details about my simulation.
I have glucose molecule in my system. I am interested in change in dipole
moment of OH bond of glucose along the simulation.
I have made the index file.
How can I select two groups (oxygen and hydrogen) or should I put
particular
On 2011-05-25 18.03, Nilesh Dhumal wrote:
Thanks for reply.
Here are more details about my simulation.
I have glucose molecule in my system. I am interested in change in dipole
moment of OH bond of glucose along the simulation.
The OH group is not neutral so your dipole is meaningless
Basically I want to calculate the stretching vibration of the bond by
fourier transfrom of dipole momenet autocorrelation fucntion or velocity
autocorrelation function.
Before going for vibration I wanted to check the fluctuation of dipole
moment along the simulation.
Can I calculate the
On 2011-05-25 20.42, Nilesh Dhumal wrote:
Basically I want to calculate the stretching vibration of the bond by
fourier transfrom of dipole momenet autocorrelation fucntion or velocity
autocorrelation function.
Before going for vibration I wanted to check the fluctuation of dipole
moment along
On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:
Hi,
I have a long-chain peptide which has a net charge of +5 . I was
wondering whether the g_dipole will give any reasonable dipole moment
for a molecule with a net charge. Is there any suggestion I should
follow regarding calculation of
Dommert Florian skrev 2011-04-01 09.45:
On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:
Hi,
I have a long-chain peptide which has a net charge of +5 . I was
wondering whether the g_dipole will give any reasonable dipole moment
for a molecule with a net charge. Is there any suggestion I
On Fri, 2011-04-01 at 09:48 +0200, Erik Marklund wrote:
Dommert Florian skrev 2011-04-01 09.45:
On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:
Hi,
I have a long-chain peptide which has a net charge of +5 . I was
wondering whether the g_dipole will give any reasonable dipole
On 2011-01-25 14.51, Olga Ivchenko wrote:
Dear gromacs users,
I would like to ask if there is a possibility in gromacs to calculate
dipole moment between two atoms. For example one from water and another
one from ligand.
best,
Olga
If you mean the combined dipole moment of a particular water
Dear David,
I mean a dipole moment between a particle atom in a ligand and a particular
atom in water molecule. G_dipoles works for molecules, as I understood, not
for atoms.
best,
Olga
2011/1/25 David van der Spoel sp...@xray.bmc.uu.se
On 2011-01-25 14.51, Olga Ivchenko wrote:
Dear
On 2011-01-25 16.01, Olga Ivchenko wrote:
Dear David,
I mean a dipole moment between a particle atom in a ligand and a
particular atom in water molecule. G_dipoles works for molecules, as I
understood, not for atoms.
You can measure the distance between them, the dipole moment will be
Thank you David,
Olga
2011/1/25 David van der Spoel sp...@xray.bmc.uu.se
On 2011-01-25 16.01, Olga Ivchenko wrote:
Dear David,
I mean a dipole moment between a particle atom in a ligand and a
particular atom in water molecule. G_dipoles works for molecules, as I
understood, not for
On 2010-08-26 18.59, Chih-Ying Lin wrote:
Hi
The partial charges of the trans and cis azobenzene are given as point
charges lied on each atom center in my MD simulation.
and where do you get the charges from?
It is supposed that the real molecule of trans-azobenzene has a lower
dipole
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