Hi
To see folding events in your (very) long peptide in explicit solvent,
without doing long MD ( 100 ns), you will need to use more complex MD
approach such as REMD or metadynamics. REMD is implemented in gromacs, but
for the latter one, you can use plumed with GROMACS.
See for example
Dear All,
A quick question, here
g_angle with the -oc word can compute the dihedral correlation function C(t)
as well as g_chi with -corr argument . Do these tools use the same approach
discussed in the paper of van der Spoel and Berendsen 1997 BJ 72 2032.to
compute C(t) ?
Thank you for the
Hi GMX users,
I am interesting to compute the tcf of C-H bonds for several surfactants in
micelles. Is there a tool in GROMACS to do that ?
Stephane
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Hi everybody,
I would like to compute the translational diffusion around the micelle
surface. I know that I can select the water molecules at x distance of the
micelle surface with g_select (right ?) but how to use this file generated
by g_select to compute de diffusion, since the index
Hi,
I suggest taking a look in RED.DB web site
(http://q4md-forcefieldtools.org/REDDB/index.php), where some RESP charges
for DNA are stored.
HTH
Stephane
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Message: 1
Date: Tue, 31 Jan 2012 16:11:02 +1100
From: Mark
Hi all,
For a future project, I would like to use gromacs for simulations with the
CHARMM force field. I am aware that the CHARMM ff is not yet officially
supported by gromacs, even if a paper about this port will be published
soon. By reading the mailing list, I understand that a beta
Hi Par,
Thank you so much for your explanations, it is very helpful.
Stéphane
Hi Stephane,
I am doing some tests with the CHARMM port in GROMACS. Before to start
more extensive simulations with this ff
I have performed a short run of 1000 TIP3-CHARMM water molecules in a
cubic during
Aargh !! it is not easy :(((, I will try, your trick, Chris. By the way,
thank your for pointing the paper.
A bientot
Stéphane
Message: 5
Date: Thu, 28 Apr 2011 10:45:17 -0400
From: chris.ne...@utoronto.ca
Subject: [gmx-users] Use different fudgeLJ and fudgeQQ values in
Dear All,
For verification purposes, I would like to obtain in a readable format the
list of the pairtypes values for a molecule generated by grompp when the
gen-pairs directive is set to yes in forcefield.itp file. It is possible
? If yes, how?
Thank you in advance for your response
Thank you Mark for the commands. It is indeed what I want.
Stephane
On 9/08/2011 10:23 PM, intra\sa175950 wrote:
Dear All,
For verification purposes, I would like to obtain in a readable format
the list of the pairtypes values for a molecule generated by grompp
when the gen-pairs
Thank you Mark for the commands. It is indeed what I want.
Stephane
On 9/08/2011 10:23 PM, intra\sa175950 wrote:
Dear All,
For verification purposes, I would like to obtain in a readable format
the list of the pairtypes values for a molecule generated by grompp
when the gen-pairs
Dear All,
Few years ago, C. Neale (thanks to him!) posted in the GROMACS mailing list
a very useful tutorial [1] to scale the Coulombic 1-4 interactions when we
combine forcefields with different fudgeLJ and fudgeQQ values. I am trying
to apply this trick to a system containing a peptide and a
gmx-users@gromacs.org
Message-ID: 4e43e7d2.6050...@anu.edu.au
Content-Type: text/plain; charset=iso-8859-1
On 12/08/2011 12:16 AM, intra\sa175950 wrote:
Dear All,
Few years ago, C. Neale (thanks to him!) posted in the GROMACS mailing
list a very useful tutorial [1] to scale the Coulombic 1-4
Dear All,
I try to apply the half double pair list method for a system containing a
glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB
force field. Briefly what I did :
1- I have changed the forcefield.itp like this
[ defaults ]
; gen_pairs set explicitly
Hi Chris,
Sorry to repost the same question, but I have really tested your method the
last few weeks. My question about the gen-pairs directive come from the fact
that I have read a message from you
http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html
Where you detailed how
Dear All
I use the g_clustersize to examine the cluster decay vs. time during the
aggregation process of glycolipids into a micelle with the following
command:
$WORKDIR/gromacs-4.5.3/bin/g_clustsize_mpi -f *.xtc -s run_1.tpr -mc
bDM-AMBER99SB-ILDN-Self_b_cluster.xvg -nc
from your xtc file and
then run the analysis tool on the single snapshot file.
/Flo
On Tue, 2011-09-06 at 12:12 +0200, intra\sa175950 wrote:
Dear All
I use the g_clustersize to examine the cluster decay vs. time during
the aggregation process of glycolipids into a micelle
Dear GMXusers,
I would like to reproduce the results obtained in the paper of Marrink et al
Molecular dynamics simulations of the kinetics of spontaneous micelle
formation. J. Phys. Chem. B, 104:12165-12173, 2000. In this (old but
interesting) work, the authors used the GROMOS96 force field to
Shame on me!!
Indeed, you are right Justin. I have misread the paper. I don't know why I
cited GROMOS96. Sorry all for wasting your time with these silly questions.
Stephane
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Hi all
For a research project, I need to know how gromacs work/scale (especially
gmx 4.0.4) in SGI ALTIX ICE 8200 EX machine cluster with Intel Quad-Core
E5472. I want to simulate a molecular system (with 14 amino acid peptide +/-
5000 water molecules) in explicit conditions with PME and 32
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