Dear gmx users,
I'm curious about how to determine the magnitude of reciprocal vectors in
normal Ewald summation.
Take the example in the manual(4.6.5), the box length is 3nm and Fourier
spacing is 0.6, then it says there will be 11 wave vectors in each
direction.
How to get this value?
--
Sincer
Hi,
Not sure if it was also you, but I recall replying not so long ago to a QM/MM
question that all QM atoms must by inside the same topology (itp or top) for
gromacs 4 and beyond. Splitting the QM atoms over multiple topologies leads to
erroneous behaviour.
I don't know for sure if this is a
Hi..
Thanks for the reply. I was unable to download gromacs-5.1.2; when i
clicked on the link, it showed "the site can't be reached."
However I have been able to figure out the solution. The trajectory file I
was using for analysis of protein-solvent hydrogen bonds did not contain
water coor
-- Forwarded message --
From: soumadwip ghosh
Date: Wed, Apr 27, 2016 at 2:52 PM
Subject: Simulation getting slower and ultimately crashing
To: "gromacs.org_gmx-users"
Hi,
I am simulating a nucleic acid in the presence of a 15X15 single
walled carbon nanotube using CHARMM 2
Dear Gromacs users!
To detect different binding sites of the assosiation between two
proteins during 10 independent md runs I would like to i) combine all
of my MD trajectories together and center the receptor protein {which
is consisted of 10 chains determined as 10 .rtp files within
topology.t
Sir, I am running a simulation for 50ns for a protein separately and also
with a ligand docked to the protein. The mdp files and all are same for
both the run , but however while running the protein its taking only
around 3 days while running the protein-ligand docked complex its taking
around 7 da
Hello everyone,
I would like to know if the prescribed settings for CHARMM36
(http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM),
specifically regarding constraints = h-bonds, apply to all steps (em,
nvt, npt, etc). I am assuming so, but I am asking because setting
constra
On 4/28/16 5:21 PM, Gregory Poon wrote:
Hello everyone,
I would like to know if the prescribed settings for CHARMM36
(http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM),
specifically regarding constraints = h-bonds, apply to all steps (em, nvt, npt,
etc). I am assuming so,
Hello,
In umbrella sampling simulations I have observed unusual unfolding events,
which appear after restarting simulations.
I have simulated a homo-dimer with about 150 residues for each monomer. The
system has been set up with TIP3P explicit solvent and the CHARMM22* force
field.
In the umbrell
Dear All,
Here I have 2 questions related to the ligand.gro and ligand.itp preparation
for the md of protein-ligand complex.
First, we have different ways to get the ligand.itp by different serves which
use different electronic charge assignment methods. Is any difference for the
md result f
10 matches
Mail list logo