Hi, dear all (especially for David):
When reading the paper "Thermodynamics of hydrogen bonding in hydrophilic
and hydrophobic media" and its supplementary material and the code
"gmx_hbond.c" for the analysis of hydrogen bond, I got questions:
1. When calculating the autocorrelation function of the
Stefan Hoorman wrote:
Stefan Hoorman wrote:
>
> Stefan Hoorman wrote:
> > How can I calculate the angle between a helix inserted in a
> membrane and
> > the axis perpendicular to the surface of the membrane. I
have tried
> > using g_h
Jack Shultz wrote:
Even though I can sucessfully run this when I remove the verbose flag,
it causes another problem. We keep trac of the progress of indivual
simulations using a code modfication in sim_util.c
124: f = fopen("progress.txt", "w");
125- if (!f) return;
126- fprintf(f
Vitaly V. Chaban wrote:
On Sat, Dec 5, 2009 at 10:40 PM, Justin A. Lemkul wrote:
Vitaly V. Chaban wrote:
Hi,
Is there a way to output only intramolecular interaction (LJ and
Coulomb but not bond, angle, etc) energies (with a respect of
exclusions, of course). It seems LJ-(SR) and Coulomb-(
On Sat, Dec 5, 2009 at 10:40 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Hi,
>>
>> Is there a way to output only intramolecular interaction (LJ and
>> Coulomb but not bond, angle, etc) energies (with a respect of
>> exclusions, of course). It seems LJ-(SR) and Coulomb-(SR) term
Vitaly V. Chaban wrote:
Hi,
Is there a way to output only intramolecular interaction (LJ and
Coulomb but not bond, angle, etc) energies (with a respect of
exclusions, of course). It seems LJ-(SR) and Coulomb-(SR) terms in
g_energy include all interaction, both inter- and intramolecular ones.
Hi,
Is there a way to output only intramolecular interaction (LJ and
Coulomb but not bond, angle, etc) energies (with a respect of
exclusions, of course). It seems LJ-(SR) and Coulomb-(SR) terms in
g_energy include all interaction, both inter- and intramolecular ones.
Thanks,
Vitaly
--
gmx-users
Hi there,
I'm back to gromacs after some time and I'm trying to build a periodic single
wall armchair nanotube with gromacs 4.0.5.
I decided to start from scratch, writing my own set of .atp, .rtp, itp files
based on oplsaa forcefield, as I was used to do before for polymers.
I have already red
Even though I can sucessfully run this when I remove the verbose flag,
it causes another problem. We keep trac of the progress of indivual
simulations using a code modfication in sim_util.c
124: f = fopen("progress.txt", "w");
125- if (!f) return;
126- fprintf(f, "%g", (step - ir->i
>
> Stefan Hoorman wrote:
> >
> > Stefan Hoorman wrote:
> > > How can I calculate the angle between a helix inserted in a
> > membrane and
> > > the axis perpendicular to the surface of the membrane. I have
> tried
> > > using g_helixorient, but the graphs all come as a strai
pawan raghav wrote:
When defining the box dimention then how do I know about the distance of
protein from the box wall? Which should be greater than half of the
You know because you specify it with editconf -d :)
Cut-Off (1.4nm) (according to some tutorial).
This solute-wall distance is
When defining the box dimention then how do I know about the distance of
protein from the box wall? Which should be greater than half of the Cut-Off
(1.4nm) (according to some tutorial).
Then what are longest cutoff which must be shorter than half the shortest
box vector to satisfy the minimum ima
But my system is rigid benzene molecule, and all intramolecular
interactions are absent.
The RF modifies a short-range electrostatic potential. Is it correct
for both decoupling scheme and "manual" method? Where is the
difference? And what about additive constant (named Crf in the manual,
formula 4
13 matches
Mail list logo
