代振宇 wrote:
Hello, everyone:
Would you please tell me that whether Gromacs can be used to do Molecular
Dynamics studies for Polymer like PVC or PET? Thanks a lot.
yes if you provide the input files. gromacs does not have many tools to
deal with preparing input files for such systems, but
Dear gmx users,
When I am minimizing a trimer protein in vacuum by SD as well as CG methods,
one of the monomer gets apart from the rest of the protein and places itself
away from the other two monomers, which are intact. No periodic box is
assigned. But when I am running editconf and assigning
[EMAIL PROTECTED] wrote:
Dear gmx users,
When I am minimizing a trimer protein in vacuum by SD as well as CG methods,
one of the monomer gets apart from the rest of the protein and places itself
away from the other two monomers, which are intact. No periodic box is
assigned. But when I am runn
Hi Dear users, I have started to do calculations of the binding between
a protein and different ligands. I have read articles on the LIE method
and one tutorial. But still I have some quite general questions. I am
using Cut-off and NVT ensamble.
1. When I run my ligands in a water solution without
ure. Nature is more
complicated than language or mathematics. Nevertheless, one must do
one's best to produce a set of symbols which are not to discordant with
the facts.
J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 19
[EMAIL PROTECTED] wrote:
Hi David,
I have checked the mdout.mdp and as you said it has pbc = xyz. What do
I do now. I havent run editconf, but why it is taking pbc conditions? How
do I remove these??
pbc=no
thanks
Anwar
--
Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Na
Dear All who may concern, I have some questions for the
charge calculation in Gromacs, I used the forcefied ffG43a1 for the
protein and inhibitors. Does the charge for the protein is the charge
per residue? This forcefield is just for the polar H, right? For the
nonpolar H, it will merge the H
> Dear All who may concern,
> I have some questions for the charge calculation in Gromacs, I used
> the
> forcefied ffG43a1 for the protein and inhibitors. Does the charge for the
> protein is the charge per residue?
The charge on a residue is the sum of the charges on the (united) atoms
that
Title: Viscosity in PE
Dear Gromacs-users
I have already run some MD, both in NVT and NPT, of Polyethylene (1000 atoms-backbone).
I would like to estimate the viscosity of my systems. Is it possible even if it is a rubbery solid? Which method is the most suitable?
Regards
Alessandro Mattoz
If you can't write a script, then do the minimization and equilibration with
water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y) or
use constraints in the z dimension (posre.itp force constant 1000 along z and 0
along x and y). This will stop it from going into the membrane.
You can calculate it from the velocity autocorrelation function, which
can be calculated using the g_velacc. The friction can be calculated
from the integral of the velocity autocorrelation function
(friction=3KbT/(integral of vacf)) and then the viscosity can be
calculated using Stoke's equati
Dear All..to continue the run, as i understood, I modified the md.mdp and then use the .tpr and .trr for the further run. Can anyone suggest that it is the right way or not? actually in one of the tutorials note i have just found to change the options as -time $value -until $value. I was wondering
Dňa Št 7. September 2006 15:27 Navratna Vajpai napísal:
> Dear All..
> to continue the run, as i understood, I modified the md.mdp and then
> use the .tpr and .trr for the further run. Can anyone suggest that it
> is the right way or not? actually in one of the tutorials note i have
> just found to
Hello Chris
So you mean to do a constrained MDS to let the lipids "fill the gaps"
between the box edges and lipids, after that do a unconstrained MDS,
then we'll get a fine structure, am I right?
Thank you very much, I'll try that
Xin Liu
On 9/7/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
Esther Caballero-Manrique wrote:
You can calculate it from the velocity autocorrelation function, which
can be calculated using the g_velacc. The friction can be calculated
from the integral of the velocity autocorrelation function
(friction=3KbT/(integral of vacf)) and then the viscosity can b
Dear all,I did a massive MD simulation of nanostructure. In my calculation, over 80% atoms have zero charge and the main CPU time is devoted to Coulomb interaction. I wonder if anyone knows how to exclude these neutral atoms from Coublomb interaction so that a lot of CPU time will be saved.Many tha
Dear gmx-ersI have attemped to use the potential of Buckingham to simulate the
water liquid. However I did not find papers that present the
parameters of the potential. Actually I found a paper that mixed parameters LJ (O...O) and Buckingham (O-H, O-O and H...O).
Can anyone let me know if there is
On Thursday 07 September 2006 23:18, Eudes Fileti wrote:
> Dear gmx-ers
> I have attemped to use the potential of Buckingham
> to simulate the water liquid. However I did not find
> papers that present the parameters of the potential.
> Actually I found a paper that mixed parameters LJ (O...O)
> an
Having actually looked back at my notes, here is what I did to extend pope.pdb
into a larger system. However, the suggestion that I posted last time should
work just as well.
1. Remove all waters
2. Duplicate the box until your heart's content. Make it larger than you
actually want because the
From: David van der Spoel <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Viscosity in PE
Date: Thu, 07 Sep 2006 19:36:34 +0200
Esther Caballero-Manrique wrote:
You can calculate it from the velocity autocorrelat
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