On 02/05/17 06:06, Mohsen Ramezanpour wrote:
Hi Everyone,
I would like to know your opinion on these questions.
I highly appreciate your comments in advance.
You could at least at the address of the server and tell in one line
what it is supposed to do.
You should never mix force fields
On 01/05/17 18:44, Saumyak Mukherjee wrote:
Dear Users,
Can anybody please tell me how to calculate the volume of protein hydration
layer as a function of time? Apart from this I would also like to calculate
the volume of second hydration shell around a protein.
I can define hydration layer in
Hi Everyone,
I would like to know your opinion on these questions.
I highly appreciate your comments in advance.
Cheers,
Mohsen
On Thu, Apr 27, 2017 at 10:23 PM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> Dear Gromacs users,
>
> Using GAAMP server for parameterization, if the
On 5/1/17 1:05 PM, Chetan Puri wrote:
Is there any example or tutorial for building a polymer topology/itp file.
First Google result for "GROMACS polymer" is
http://www.gromacs.org/Documentation/How-tos/Polymers :)
-Justin
--
==
Justin A.
On 5/1/17 10:15 AM, Marcelo Depólo wrote:
Hi!
I am running ACF calculations in gmx hbond tool in 5.0.7 version.
When running:
gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg
and
gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg
The results given for
Hi,
I am not sure how to interpret the cos(theta1) around my reference atom.
The help printed is not straightforward when comes to set which atoms forms
the angle theta1. For instance.
"theta_1: the angle with the vector from the first atom of the solvent
molecule
to the midpoint between atoms
Is there any example or tutorial for building a polymer topology/itp file.
I need for PVP.
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Dear Users,
Can anybody please tell me how to calculate the volume of protein hydration
layer as a function of time? Apart from this I would also like to calculate
the volume of second hydration shell around a protein.
I can define hydration layer in two ways:
1. g_select
2. trjorder
If this
Hi!
I am running ACF calculations in gmx hbond tool in 5.0.7 version.
When running:
gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg
and
gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg
The results given for the ACF are completely different (example:
Dear Mark
First apology that I am unaware how to run the test programs.
Next, I tried to simulate a protein and i get the following error.
*[user@mqml rahul]$* source /usr/local/gromacs/bin/GMXRC
*[user@mqml rahul]$* gmx pdb2gmx -f 99nsInput.pdb -o 99nsInput.gro -p
99nsInput.top
gmx:
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