Good morning, Mark!
How do I officially request this as a feature of the next version of
GROMACS? Post to the developers' forum?
Thanks,
Inon.
On Saturday, December 24, 2011 12:24:11 PM UTC+2, Mark Abraham wrote:
On 12/24/2011 6:23 PM, Inon Sharony wrote:
Good morning!
I'm running GMX
Dear All,
I have a problem running gromacs for a oligosaccharide. it has 14
units sugars containing glucose, mannose and N-acetyl glucosamine
units. I want to do MD simulations for this with opls aa force field.
For this I have generated the .itp files using topolgen (edited the
atoms according
Op 25 dec 2011 om 09:21 heeft Inon Sharony inons...@tau.ac.il het volgende
geschreven:
Good morning, Mark!
How do I officially request this as a feature of the next version of GROMACS?
Post to the developers' forum?
Your best bet is to implement it yourself and test it and send a
Dear all;
As you all know, in all of the force fields in Gromacs package, G,C,A and T
are known. In your opinion, what should I do in case of 8-OxoG? How to obtain
parameters needed for this new residue?
Thank you
B.Mehrazma
From: Mark Abraham
Dear all,
with great pleasure I am announcing the GROMACS Molecule Liquid
Database at http://virtualchemistry.org.
The website holds *validated* itp files and liquid structures for 146
molecular liquids. For all liquids eight different simulated properties
and (where available)
Dear teacher,
how to use gromacs 4.5.5's temple?
i make the temple successful! And when i run it (./template -f traj.xtc -s
water.tpr -cutoff 2),
the output like this:
Reading file water.tpr, VERSION 4.5.5 (single precision)
Reading file water.tpr, VERSION 4.5.5 (single precision)
Specify a
Dear
I want to simulate cell membranes in weightlessness condition ( the same as
space).Would you please tell me Can I run with Gromacs? If Yes with which
parameters?
Best
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the
On 2011-12-25 14:30, Shahrbanoo Karbalaee wrote:
Dear
I want to simulate cell membranes in weightlessness condition ( the same
as space).Would you please tell me Can I run with Gromacs? If Yes with
which parameters?
Best
It is weightless by default! Isn't that great? But seriously for most
Hello
I took parameters that are calculated for a charmm22 forcefield and I want to
use it with a charmm27 forcefield (I have the same molecule as the people who
calculated the charmm22 parameters but they didn't use gromacs). I made a
.rtp, .hdb and residuetypes.dat file and edit the
Lara Bunte wrote:
Hello
I took parameters that are calculated for a charmm22 forcefield and I
want to use it with a charmm27 forcefield (I have the same molecule as
the people who calculated the charmm22 parameters but they didn't use
gromacs). I made a .rtp, .hdb and residuetypes.dat
Hello
I have a few questions about molecular dynamics simulations.
1) For a molecule Newton's equation of motion is solved. Do I get here one
resulting force for the hole molecule or do I get a lot of forces, one for each
atom?
2) The force is calculated from the potential. This consists of
Lara Bunte wrote:
Hi,
first thanks for help. I have two questions.
1.) Is this mail going to the mailing list or only to you? If only you
get it, how to answer in my thread in the mailig list?
The mail went to the mailing list. Respond to the post by sending to
gmx-users@gromacs.org.
Lara Bunte wrote:
Hello
I have a few questions about molecular dynamics simulations.
1) For a molecule Newton's equation of motion is solved. Do I get here
one resulting force for the hole molecule or do I get a lot of forces,
one for each atom?
Forces per atom at each timestep can be
On 12/26/2011 7:45 AM, Lara Bunte wrote:
Hello
I have a few questions about molecular dynamics simulations.
1) For a molecule Newton's equation of motion is solved. Do I get here
one resulting force for the hole molecule or do I get a lot of forces,
one for each atom?
2) The force is
On Sun, 25 Dec 2011 20:45:44 + (GMT)
Lara Bunte lara.bu...@yahoo.de wrote:
Hello
I have a few questions about molecular dynamics simulations.
1) For a molecule Newton's equation of motion is solved. Do I get
here one resulting force for the hole molecule or do I get a lot of
forces,
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