Dear gmxers,
I have reinstalled the gmx-4.5.1 and this time the pdb2gmx is found to work
using the same input and parameter files. So I consider that the very strange
problem is due to some modified file which is unknown yet for me. Thanks again
for your attention.
Sincerely, yours
Chaofu
On 2010-10-19 02.01, Chih-Ying Lin wrote:
Hi
From David =
dipole is 48.0 sum of q_i x_i, therefore if you
have large charge separation you will get a large dipole.
1. What does the coefficient 48.0 represent?
Unit conversion from e nm to D.
2. Is q_i = partial charge or charge on the
Hi,
Fatal error:
[ file protein.itp, line 9 ]:
Atom index (5) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
position_restraints
in a part belonging to a different molecule than you intended to.
In that case move the position_restraints
Hi,
I would allow flexible water by uncommenting the line
define = -DFLEXIBLE
and trying again; reducing the time step might also be required.
Message: 4
Date: Mon, 18 Oct 2010 16:26:16 -0400
From: Sai Pooja
Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want
to read the part about calculating dipole moments for an array of point
charges, it is not difficult. 33 point charges are doable using pencil
and calculator in about 10min. Do not worry about the reference point as
long
On 18/10/10 13:06, Mark Abraham wrote:
On 18/10/2010 10:53 PM, ms wrote:
On 18/10/10 03:30, Mark Abraham wrote:
Mark,
Thanks a lot for cc'ing me the bugzilla report. Do you think it is
related to the problems I have? (well, for sure bugs can't help, but...)
thank you!
m.
--
Massimo
Hi gromacs users
Can I use gromacs for obtaining Gibbs free energy of binding of protein and
dna?
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Hi,
I'm installing GROMACS 4.5.1 on our Intel Nehalem/InfiniBand cluster and
wish to install both single and double precision versions.
Am I correct in thinking that the same libraries are built, both with or
without --enable-double, and it's just the binaries that are different
(and
#ZHAO LINA# wrote:
Hi,
Fatal error:
[ file protein.itp, line 9 ]:
Atom index (5) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
position_restraints
in a part belonging to a different molecule than you intended to.
In that case move
shahab shariati wrote:
Hi gromacs users
Can I use gromacs for obtaining Gibbs free energy of binding of protein
and dna?
Yes. I would suggest you read about potential of mean force calculations.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
As I say continually, I am not a private tutor. Please keep all Gromacs-related
correspondence on the gmx-users list. I am CC'ing this message there and would
ask that any further discussion be held in this forum.
Binding energy is not trivial to calculate, and will require some type of
Shahab,
Justin is entirely correct, you should read about potential of mean
force calculations, the gromacs pull code, and the gromacs free energy
code.
However, an important question is if you can *converge* the free
energy of macromolecular binding. If you don't know the bound state,
Hi all,
There is a problem that I encountered when I was trying to manually
verify the proper dihedral conversion from AMBER topology to GROMACS
topology using amb2gmx perl script.
Some of the dihedrals were set to zero by amb2gmx even if in the
prmtop file they were not zero. This was happening
Hi All,
I was wondering if it is possible to pull on a single chain? I would like to
anchor the C-terminus and pull the N-terminus and have a plot of pulling force
vs displacement.
I'm looking for more or less a yes or no answer, if you would like to elaborate
then I won't complain :)
or less a yes or no answer, if you would like to
elaborate then I won't complain :)
Thanks,
Joe
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Dear all,
I want to use umbrella sampling to calculate the PMF of the
conformational transition of a protein. What temperature coupling method and
pressure coupling method should I use? Berendsen temperature coupling or
Nose-Hoover temperature coupling? Or each one is OK?
--
gmx-users
Use Langevin dynamics (the sd integrator) to control the temperature.
You are sure to get the correct ensemble that way and if you are doing
US then you can not extract dynamics anyway.
Hopefully somebody else can address the pressure coupling for you, but
probably you need to provide more
Hi Roland,
I did as you suggested and it worked fine!
Thanks,
Renato
2010/10/15 Roland Schulz rol...@utk.edu:
You should use the latest GROMACS version also for the GPU. Thus compile the
4.5.1 for the GPU and run this.
On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas renato...@gmail.com
.
I'm looking for more or less a yes or no answer, if you would like to
elaborate then I won't complain :)
Thanks,
Joe
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Warren,
You're right that one can not use constraints if they are also using lincs on
C-C bonds.
However, constraining this bond is not necessary with a 1 fs timestep.
Even while constraining C-C bond lengths, one can still use harmonic restraints
instead (also from the pull code).
Before
Message: 6
Date: Tue, 19 Oct 2010 09:30:47 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Umbrella sampling with temperature and
pressurecoupling method problem
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
Hi
Is there a way to create pinned dipoles in Gromacs? I.e. to pin a point dipole
to a molecule with an orientation? I've looked in the manual but find nothing
or online. Also is there any provision for SSD [soft sticky dipole] water
molecules?
Thanks
Brett--
gmx-users mailing list
On 2010-10-19 18.40, Donovan B.T. wrote:
Hi
Is there a way to create pinned dipoles in Gromacs? I.e. to pin a point dipole
to a molecule with an orientation? I've looked in the manual but find nothing
or online. Also is there any provision for SSD [soft sticky dipole] water
molecules?
No
DeChang Li wrote:
Message: 6
Date: Tue, 19 Oct 2010 09:30:47 -0400
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] Umbrella sampling with temperature and
pressurecoupling method problem
To: Discussion list for
Hi,
I've got a top2psf.pl script from the web and used it to generate a psf file.
Yet it generated some bonds to atoms with index 0 which should not occur. It
causes VMD cannot load it and had a segmentation fault.
vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf
Kwee Hong wrote:
Hi,
I've got a top2psf.pl script from the web and used it to generate a psf
file. Yet it generated some bonds to atoms with index 0 which should
not occur. It causes VMD cannot load it and had a segmentation fault.
vmd Info) Using plugin psf for structure file
Kwee Hong wrote:
I executed the script at the therminal by typing
perl top2psf.pl -i topol.top -o zz.psf
Here, I attached my input file.
Your topology does not correspond to a MARTINI coarse-grained topology. As
such, probably a bunch of the pattern matching is getting incorrect
On 27/09/10 21:18, Sai Pooja wrote:
Thanks M!
I am using the standard 6-12 tables available with the gromacs package. For
-table and -tablep options to start with.
I want to understand 1 thing. The forcefield files and the topology file
specifies sigma and epsilon parameters. If I change the
Hi
I had developed couple of post processing/analysis codes in earlier version
of gromacs4.0.7.
Now I have upgraded to gromacs4.5.1 and when I check its template file , its
completely different that the earlier version. Does that mean old
post-processing codes have to rewritten if I were to use
Also, will there be any errors if I use trajectory computed by gromacs4.5.1
and use post processing code developed for gromacs4.0.7. I plan to keep both
versions of gromacs installed on my system, until I get fully comfortable
new version!
On Tue, Oct 19, 2010 at 4:14 PM, Sikandar Mashayak
Hello all,
I noticed significant changes in my simulation results between running gromacs
4.5.1 with the included amber-gs-s force field and gromacs 4.0.7 with Eric
Sorin's amber ports. I eventually figured out that the parameter files in the
amberGS.ff directory are identical (up to
Message: 5
Date: Tue, 19 Oct 2010 13:06:42 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Re: Umbrella sampling with temperature and
pressurecoupling method problem (Justin A. Lemkul)
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi
molecule dipole is 48.0 sum of q_i x_i
For a multiple-atoms molecule, the dipole moment of a covalent bond is a
vector, parallel to the bond axis,
For a multiple-atoms molecule, which includes a ionic bond, how to determine
the direction of ionic bond dipole moment in theory ?
How does
?
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