Hi Gurunath,
You have to run both simulations for (approximately) infinite time and
compare the probability density functions to check whether the simulations
are the same. Maybe running more simulations would also be a good idea.
Here's something about simulations and statistics:
Dear All,
I'm trying to examine the association of amino acid (gamma amino
butric acid) in a non-polar solvent (trifluoroethanol).
I calculated the PMF for three different concentrations of amino acid
in solution along the distances between GABA molecules.
Despite the fact that, increasing
First define and calculate the native contacts (contacts which were present
in native reference structure and exist for significant amount of time
during simulation). Then you can identify the contacts which exist for
significant amount of time but were not present in native reference
structure
On 1/15/14, 7:14 AM, rajat desikan wrote:
Hi All,
I was wondering about the long range electrostatics while calculating
single point energies. I did a cursory calculation for a protein in water
(PME) and found that the LR electrostatic terms were zero. I know that the
per-particle
Hi all
I have DOPC lipid in my system. After preparing index file exactly based on
how-to on the g_order page, I used following command to obtain order
parameters of acyl chains:
g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o
order_sn1.xvg
I encountered following warnings:
Hello,
I was under the impression that pdb2gmx was supposed to referance the
force fields as defined in oplsaa.ff/forcefield.itp, but it doesn't seem
to be for me.
To double check, I removed all force field parameters from forcefield.itp
and pdb2gmx still ran and got the same result as before.
Hello:
I found that the -norandom option in genion was no longer in 4.6.5:
genion -h
Option Filename Type Description
-s topol.tpr InputRun input file: tpr tpb tpa
-n index.ndx Input, Opt. Index
Hi Justin,
I used the following commands:
mdrun_mpi -s md_6_50ns.tpr -rerun md_6_50ns.gro
gmxdump_mpi -e ener.edr ener_readme
And in the dump of the ener_readme file, I have the following terms:
Coul-SR:Protein-Protein -6.62324e+05
LJ-SR:Protein-Protein -5.64854e+04
Coul-14:Protein-Protein
On 1/15/14, 9:30 AM, shahab shariati wrote:
Hi all
I have DOPC lipid in my system. After preparing index file exactly based on
how-to on the g_order page, I used following command to obtain order
parameters of acyl chains:
g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o
On 1/15/14, 10:52 AM, Albert wrote:
Hello:
I found that the -norandom option in genion was no longer in 4.6.5:
genion -h
Option Filename Type Description
-s topol.tpr InputRun input file: tpr tpb tpa
Hi,
I have never done this before. But is this a possibility?
http://www.pymolwiki.org/index.php/Contact_map_visualizer
On Wed, Jan 15, 2014 at 8:41 PM, bipin singh bipinel...@gmail.com wrote:
Hello Dr. Justin,
Yes, there is no in-built module in Gromacs to get the information about
native
Dear Gmx Users,
Is there any way in Gromacs to scale tabulated potentials from
energygrp_table (non-bonded)?
Steven
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Hey Fra,
if you have a few minutes could you maybe help me with some trouble I have
with gaia? (session login seems to be corrupt / firefox cannot be started
since it thinks I am still logged in seomwhere else)
Best,
Marc
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Best, Marc Hoemberger
On Wed, Jan 15, 2014 at 5:01 PM, Marc Hömberger hoe...@gmail.com wrote:
Hey Fra,
if you have a few minutes could you maybe help me with some trouble I have
with gaia? (session login seems to be
Yes, they get multiplied by parameters like charge, C6, C12 etc. Is that
the question you're asking? :-)
Mark
On Wed, Jan 15, 2014 at 8:02 PM, Steven Neumann s.neuman...@gmail.comwrote:
Dear Gmx Users,
Is there any way in Gromacs to scale tabulated potentials from
energygrp_table
On 1/15/14, 4:18 PM, rajat desikan wrote:
Hi Justin,
Thanks for the reply. So, must I use a separate .mdp file with infinite cutoffs
for both vdw and coulomb to get all the LR interactions correctly? Can you give
me specific pointers about the settings?
Infinite cutoffs, zero steps, don't
Dear Justin Thank you For your previous reply
I would like to do REMD (Replica exchange MD) in gromacs I am very happy
if you paste tutorial for REMD, Targeted MD , Constraint MD and Non
Equilibrium MD
as
Dear Vidya sankar,
I think this may help you with the REMD. Here's the link for the tutorial:
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3a_Mark_Abraham%2c_Session_1B
This tutorial deals with REMD and
How can I impose restraints in gromacs .mdp file or topology file to
avoid isomerization of the peptide bond at the highest temperatures?
Your help is appreciated
--
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
Software has bugs, unfortunately, and GROMACS tools particularly so. We are
trying to improve the situation, but if a developer isn't using a tool, it
doesn't get any love! Are you trying to say it doesn't work in 4.6.5?
Mark
On Jan 16, 2014 5:51 AM, tarak karmakar tarak20...@gmail.com wrote:
See chapter four for what is available, and tables in 5.5 for a summary of
their use.
Mark
On Jan 16, 2014 5:11 AM, Neha Gandhi n.gandh...@gmail.com wrote:
How can I impose restraints in gromacs .mdp file or topology file to
avoid isomerization of the peptide bond at the highest temperatures?
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