On 6/24/13 1:07 PM, Sonia Aguilera wrote:
Hi all!
I have been running a series of simulations for coupling a molecule (free
energy calculations). All my settings and parameters in the mdp file worked
great for one system, but then I change the molecule to a bigger one and I
started to have
On Wed, Apr 10, 2013 at 9:51 AM, Liron Cohen liron.co...@weizmann.ac.ilwrote:
Hi,
I am using gromacs 4.5 and i am trying to run an energy minimization and
then temperature equilibration for a system of two charged plates plates
solvented in water.
the plates are made of fake atoms which has
On 4/3/13 7:16 AM, Liron Cohen wrote:
After reading the manual and trying to find more information on the mailing
list. I'm still not sure about this 1-4 interactions, when I want to calculate
the energy between two groups (lets say one residue and the rest of the
protein) should I sum
users
Subject: Re: [gmx-users] 1-4 interactions
On 4/3/13 7:16 AM, Liron Cohen wrote:
After reading the manual and trying to find more information on the mailing
list. I'm still not sure about this 1-4 interactions, when I want to
calculate the energy between two groups (lets say one residue
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: Wednesday, April 03, 2013 2:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] 1-4 interactions
On 4/3/13 7:16 AM
You can either specify this explicitly or use the fudge LJ and fudge
q headers in your topology file. See the manual for details.
On Sep 26, 2009, at 1:51 AM, Vitaly V. Chaban wrote:
Hi,
Is it possible in gromacs to make 1-4 interaction energy reduced as
compared to the intermolecular
Hi,
Thanks for the prompt responses. I checked the distance between atoms
908 and 913 in VMD and got 0.396nm, which seems fine. I thought then, that
my problem may be with my box size when I used editconf. When I changed
the box dimension to 2.0nm from the molecule periphery, the warning
toma0052 wrote:
Hi,
Thanks for the prompt responses. I checked the distance between atoms
908 and 913 in VMD and got 0.396nm, which seems fine. I thought then, that
my problem may be with my box size when I used editconf. When I changed
the box dimension to 2.0nm from the molecule
toma0052 wrote:
Hello,
I am starting simulations on a DPPC lipid bilayer taken from Peter
Tieleman's website. Upon trying to run the energy minimization, the
program runs, but the results does not appear correct. During the run, I
get the warning:
Warning: 1-4 interaction between 908 and
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