Hi
I used g_hbond for analyzing hydrogen bonds.
What is difference between [s0 legend "Ac\sfin sys\v{}\z{}(t)"] and [s1 legend
"Ac(t)"] in hbac.xvg file in below?
@title "Hydrogen Bond Autocorrelation"
@xaxis label "Time (ps)"
@yaxis label "C(t)"
@ s0 legend "Ac\sfin sys\v{
On 2/22/10 9:47 AM, leilakar...@aol.com wrote:
Hi
I used g_hbond for analyzing hydrogen bonds.
What is difference between [s0 legend "Ac\sfin sys\v{}\z{}(t)"] and [s1
legend "Ac(t)"] in hbac.xvg file in below?
First one is "corrected" for the fact that in a finite system the ACF
does not go t
pol...@huji.ac.il wrote:
Dear Justin,
Thank you for a quick replay. Do you know if there are some atom types,
charges, parameters, etc that incorporates sugar and alcohol potentials
determined by Jorgesen "OPLS all atom force field for carbohydrates"?
No clue. Have a look through the .atp
Please keep all Gromacs-related correspondence on the gmx-users list. I do not
advertise myself as a private tutor, and furthermore, archived discussions serve
the community as the whole. I am CC'ing the list in my reply; please continue
the discussion there.
Jignesh Patel wrote:
Respecte
Hello All,
I am new user of gromacs and I need to calculate the binding free energy of
a ligand and a protein. With the help of your short manual (
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial) I
maneged to run 10 ns MD for each lambda values 0, 0.1, 0.2, 0.3, 0.4, 0.5
I m trying to reproduce the same thing, by following the tutorial.
i m trying to learn the coarse grain simulation with their files, so that i
can apply for my protein.
Starting with lipids, as per their tutorial
I m just doing the steps in that tutorial, with their files,
after the genbox,
genbox
Sarath Kumar wrote:
I m trying to reproduce the same thing, by following the tutorial.
i m trying to learn the coarse grain simulation with their files, so
that i can apply for my protein.
Starting with lipids, as per their tutorial
I m just doing the steps in that tutorial, with their files,
pol...@huji.ac.il wrote:
Hi Justin,
one more question. Do yuo think I should use opls_174 or opls _175 for a
middle C of glycerol?
in atp file opls_174 12.01100 ; C(HROH): triols
opls_175 12.01100 ; C(R2OH): triols
both of them seems to be for triols and i can't understan
Dear gromacs users:
I am trying to use ffcharmm27 patched with gromacs, since it does
not have 'heme' i tried
add it manually but still i am getting error while doing pdb2gmx. If anybody
have already done 'HEME' protein using
charmm force field in gromacs, please help me. Thanks
Rama
--
Hello everybody, anyone could help me and understand why the LJ energy is
positive for
SOL-SOL interactions? The same is not true for LJ energy between benzene
(BEN-BEN) and
acetonitrile (ACN-ACN). In my opinion it should be negative considering the
analytical form
LJ potential.
Epot (kJ/mol)
Hello,
I have a run with the xtc, trr and edr files available. I would like to
color a snapshot of my system with respect to rmsd or potential energy
of my particles. How can I extract the potential energy, rmsd or any
other needed data from the files available? Is there a specific GROMACS
command
On 23/02/2010 1:03 PM, Paymon Pirzadeh wrote:
Hello,
I have a run with the xtc, trr and edr files available. I would like to
color a snapshot of my system with respect to rmsd or potential energy
of my particles. How can I extract the potential energy, rmsd or any
other needed data from the files
Paymon Pirzadeh wrote:
Hello,
I have a run with the xtc, trr and edr files available. I would like to
color a snapshot of my system with respect to rmsd or potential energy
of my particles. How can I extract the potential energy, rmsd or any
other needed data from the files available? Is there
Hello,
I like to color my particles in terms of their potential energy, rmsd,
Sg or other properties. Is there a command that can extract such
information from XTC, EDR ot TRR files?
Payman
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Ple
Dear all,
I did two md simulations of 200 particles each of a lennard-jones
fluid. One of them gave me the correct pair distribution function for a
lennard-jones fluid (converging to 1) and one did not (converging to zero).
I have attached the .mdp files for both systems below. The barosta
Lum Nforbi wrote:
Dear all,
I did two md simulations of 200 particles each of a
lennard-jones fluid. One of them gave me the correct pair distribution
function for a lennard-jones fluid (converging to 1) and one did not
(converging to zero). I have attached the .mdp files for both
On 23/02/2010 1:53 PM, Lum Nforbi wrote:
Dear all,
I did two md simulations of 200 particles each of a
lennard-jones fluid. One of them gave me the correct pair distribution
function for a lennard-jones fluid (converging to 1) and one did not
(converging to zero). I have attached the .m
Dear Gromacs users,
I simulated several imidazolium-based ionic liquids by DL_POLY code which
has three input files: CONFIG, CONTROL, and FIELD.
the force field parameter (FIELD) used from the Canongia Lopes force fields,
e.g., (OPLS_AA / AMBER based):(JPC B, 2004, Vol. 108, 2038).
now, I like co
Hi all GMX users
The viriable ra2max in the file nsc.c of lines 608-637 seems not the maximun
radii
of all the atoms. Is it right?
2010-02-23
Best
wishes！
Ji Xu
The State Key Laboratory of Multiphase Complex System
Institute of Process Engineering
Chinese Academy of Sciences
Beijing
Hi everyone,
I had been trying to work with forces of the atoms and stumbled upon
something weird.
In my md.mdp file i ask to write forces with a certain frequency then the
grompp shows a seemingly harmless note, the full md.mdp and extract of the
grompp.out are as follows :-
title
Dear Justin and all..
I have been struggled for the pass few weeks...I follow the KALP-15 in DPPC
tutorials but I am using my own protein instead.
I had successfully reached the step INFLATEGRO where 2 lipid removed from the
upper layer n 2 lipids removed from the lower layer. Then i updated my
Hi,
This note is printed when output files will be "large", large is defined as
more than 2 GB.
Not writing forces just gets you under this limit.
Berk
Date: Mon, 22 Feb 2010 23:52:13 -0800
From: kgp.a...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] writing forces in gromacs
Hi ev
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