Hi,
I am studying the dynamics of a double stranded DNA in presence of
small molecules. I want to study the preferential binding of these
molecules in the grooves and backbones of the DNA and also calculate the
feasibility of these binding in terms of calculating the free energy
change.My
Well, since you are not interested in the duplex stability, I would not use
-COM. See, during the simulation, the center-of-mass of such a small helix
part can drastically move, leading to a questionable result. Check your
system and make sure that you will not face this situation.
About the PMF,
On 12/25/14 1:43 AM, pratibha kapoor wrote:
Hi everyone,
I would like to calculate length of beta sheet. Is this any automatic tool
to serve the purpose?
To elaborate, I am aware that dssp can give me whether the residue is in
beta sheet (E) or not at each time frame but I want to know
On 12/25/14 2:49 PM, asasa qsqs wrote:
Dear Justin A. Lemkul,
I want to use pulling code for calculate the PMF of a molecule at the across the
DMPC, but i can't obtained a large pull across the membrane my pulling code was:
; Pull code
pull= umbrella
pull_geometry= position
pull_dim= N N Y
On 12/25/14 5:03 PM, Hassan Aaryapour wrote:
Dear Gromacs Users
How can I find and score protein-ligand binding poses and choose the best
pose or frame from the trajectory file after doing a Molecular dynamics
simulation of 40ns?
Best is a qualitative assessment that should be driven by
On 12/26/14 6:11 PM, Nash, Anthony wrote:
Dear Gromacs community,
Using enforced rotation potentials I have generated a really smooth rotation
of my ligand the catalytic binding domain of my protein. I then put together
a simple perl script to calculate the dihedral angle of four particular
On 12/27/14 2:05 AM, Kester Wong wrote:
Dear gmx-users,
Q1) I would like to plot the radius profile of a water droplet on graphene, as a
function of z-direction, as per below:
http://journals.aps.org/prl/article/10.1103/PhysRevLett.109.176101/figures/2/large
Which GROAMCS utility should
On 12/27/14 4:17 AM, soumadwip ghosh wrote:
Hi,
I am studying the dynamics of a double stranded DNA in presence of
small molecules. I want to study the preferential binding of these
molecules in the grooves and backbones of the DNA and also calculate the
feasibility of these binding in
Thanks for the help Justin. I've found the site:
http://membrane.urmc.rochester.edu/content/wham
Cheers
Anthony
Dr Anthony Nash
Department of Chemistry
University College London
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
Dear users
when i simulated Aspirin on Human serum albumin (pdb: 2i30)
in equilibration process (NVT), i encountered with below message and my
simulation stopped. i dont know why?
*pdfco@pdfco-X:~/Aspirin$ tail nvt.job-nex int0 Number of
random exchanges to carry out
On 12/27/14 11:42 AM, elham tazikeh wrote:
Dear users
when i simulated Aspirin on Human serum albumin (pdb: 2i30)
in equilibration process (NVT), i encountered with below message and my
simulation stopped. i dont know why?
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
A seg
Hi Justin,
I think I've shot myself in the foot and I'm trawling the gromacs manual with
little success at the moment. I'm trying to define my [ dihedral_restraint ]
over my ligand-enzyme complex. The topology of the ligand is in one .itp file
and the topology of the enzyme is in a separate
Hi all,
I am trying to calculate entropy using g_anaeig (Gromacs version 5.0.1),
after using g_nmeig to calculate eigenvectors and eigenvalues (after
computing hessian matrix):
g_nmeig_mpi -f hessian.mtx -s run.tpr -nom
g_anaeig_mpi -v eigenvec.trr -entropy
But I am getting the following
Dear gromacs users
i d like to know about charge distribution in .itp file that how can fix
the charge of atoms
for instance, i simulated Aspirin in Human serum albumin, and i want to
know about their charges
in an article charge distribution was as below, but in my .itp file
(aquired by PRODRG
Dear Justin
thanks for your advise
only my remained question is, if my problem was for my topology file (as i
recieved this error a few times: your topology file has non-zero charge =
-0.61)
by editing my topology file (.itp file), can i going on my simulation?
please tell me, what is the
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