Hi,
On Wednesday, 13. August 2008, huan wrote:
Dear all gmx-users and developers,
There are 6 different type of molecules in my simulation system. So how can
I differentiate o recognize the type of those molecules? which files
(topology, trr or others) should I look at?
Any
Date: Tue, 12 Aug 2008 16:36:16 -0500
From: Andy Shelley [EMAIL PROTECTED]
Subject: [gmx-users] Force Field Parameters Nitrogen and Oxygen
To: gmx-users@gromacs.org
Message-ID:
[EMAIL PROTECTED]
Content-Type: text/plain; charset=iso-8859-1
I am trying to simulate air and have not
Hi Andy,
To be absolutely correct air contains not only oxygen and nitrogen but
also other components, so when I mentioned about 'hard work' I meant
pointing out all the gases (and their fractions) usually present in
the atmospheric air.
As for FF, I suggest you to find original papers where O2
Hi,
Indeed this is the problem.
I have fixed it in CVS for the Gromacs 4 release.
Thanks for reporting this bug,
Berk.
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Date: Tue, 12 Aug 2008 19:51:17 -0400
Subject: [gmx-users] A bug of trjconv for force output?
Hello All,
I just
Hi everybody,
My question is regarding the consequence of a mistake of
mine.
I wanted to run gromacs with charmm force field and tip3p water model.
I had posted a query as to how can I get the tip3p.gro file. I was suggested
to equlibrate
the spc216.gro file for 1ns.
Hello,
I am doing a simulation of a membrane + protein using ffG53a6 in Gromacs.
First I equilibrated at constant volume and then I changed to semi-isotropic
pressure.
This is my mdp file:
title = EQUILIBRADO
cpp = /usr/bin/cpp
include = -I../top
define =
Hi There,
For the error I mentioned in last mail I looked in the .rtp file and .pdb
file for residue NDP. Following is the part of .pdb file showing atoms as
PA, O1A etc
HETATM 8111 PA NDP 1 8.809 -4.754 22.676 1.00 12.71
HETATM 8112 O1A NDP 1 10.106 -4.137 23.158
Message: 5
Date: Tue, 12 Aug 2008 18:21:51 -0400
From: Justin A. Lemkul [EMAIL PROTECTED]
Subject: Re: [gmx-users] Re: requested for GROMACS package
To: [EMAIL PROTECTED], Discussion list for GROMACS users
gmx-users@gromacs.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain;
Hi
I am doing a 5 peptide simulation.
I have done energy minimization using this command
1.grompp -v -f em.mdp -c b4em_sol_mov1.gro -p gnnqqny.top -o em.tpr -nice 19
2.mdrun -v -s em.tpr -e em.edr -c after_em.gro -o em.trr -g em.log -nice 19
After energy minimization (steep, 5000 steps,
huan wrote:
Dear all gmx-users and developers,
There are 6 different type of molecules in my simulation system. So how can I differentiate o recognize the type of those molecules? which files (topology, trr or others) should I look at?
If this is a simple visualization issue, it can
[EMAIL PROTECTED] wrote:
This is upto 40 ns after that i am not getting anything like that. I don't
know exactly what it mean and how could i get rid of such messages.I don't
know how to deal with it.
What it means is that you had some nasty contacts between some elements of your
system
Rebeca García Fandiño wrote:
Hello,
I am doing a simulation of a membrane + protein using ffG53a6 in Gromacs.
First I equilibrated at constant volume and then I changed to
semi-isotropic pressure.
This is my mdp file:
title = EQUILIBRADO
cpp = /usr/bin/cpp
Your output looks like, that you are doing MD simulations, because a time in ps
is reported. You should do energy minimisation first, use 'integrator = steep'
in your .mdp file
Andreas
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of [EMAIL
Vitaly Chaban wrote:
Message: 5
Date: Tue, 12 Aug 2008 18:21:51 -0400
From: Justin A. Lemkul [EMAIL PROTECTED]
Subject: Re: [gmx-users] Re: requested for GROMACS package
To: [EMAIL PROTECTED], Discussion list for GROMACS users
gmx-users@gromacs.org
Message-ID: [EMAIL PROTECTED]
Hello,
I want to simulate a membrane+proteína system (more than 700.000 atoms) with
Gromacs 4 and I would like to use 512 proc.
I am creating the mdp file with Gromacs 3, since I have read in the wiki that
it was a good way to include the number or processors ins the mdp file for the
new
Hi Rebeca,
Lines 69/70 of 3.3 include/types/simple.h reads
/* Max number of nodes */
#define MAXNODES256
This obviously needs to be set to a higher value.
There is also a MAXNODES parameter in CVS src/gmxlib/tpxio.c,
which I guess also needs to be set to the same value if
you
Hi,
I don't understand your remark about the mdp file.
Where on the wiki does it say something like this?
The number of processors is never present in the mdp file.
Just use the new version of grompp.
A week ago I have committed large changes to the CVS
which make the tpr files much smaller and
Hi Justin,
Thanx for your suggestion. But, I am not getting how to do correction in
those files I am using gromacs 3.3.3 and 1XU9.pdb molecule for my
simulation.
I am not getting what is happening in the simulation...:(...:(
kindly suggest.
With Thanx,
Vivek
2008/8/13 Justin A. Lemkul [EMAIL
vivek sharma wrote:
Hi Justin,
Thanx for your suggestion. But, I am not getting how to do correction in
those files I am using gromacs 3.3.3 and 1XU9.pdb molecule for my
simulation.
I am not getting what is happening in the simulation...:(...:(
kindly suggest.
I'm guessing that NDP is the
Hi,
This sounds like the bug in domdec.c that I fixed a month ago:
revision 1.146
date: 2008/07/11 12:09:43; author: hess; state: Exp; lines: +307 -193
fixed incorrect computation of the PME coordinate communication range with dlb
and change some formatting
Is your version from before that
Thanks a lot for your suggestion.
What I was refering was to this post:
http://www.gromacs.org/pipermail/gmx-developers/2008-February/002378.html
OR use the 3.3 grompp to produce the mdp files since it will automatically set
the fourier grid to fit the number of processors.
Sorry for not
On Thu, Jul 17, 2008 at 6:26 PM, Nicolas [EMAIL PROTECTED] wrote:
We also have a implementation of CHARMM(27) for Gromacs, but without CMAP
as well.
How is it different to the one by Mark Abraham? Is it publicly available?
The main limitation is the computational cost due to the CHARMM
Hi,
In the CVS version the fourier grid is no longer required to be divisible by
the number of processors.
But in the other mail you had fourier_nz set to zero, which is complete nonsens.
I guess you should do some reading.
Berk.
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: RE:
Dear all gmx-users and developers,
The simulation has been carried out and I cant recognize the type of molecule
since there are 6 different type of mlecules in that system.
thanks.
--- On Wed, 8/13/08, Florian Haberl [EMAIL PROTECTED] wrote:
From: Florian Haberl [EMAIL PROTECTED]
Subject:
huan wrote:
Dear all gmx-users and developers,
The simulation has been carried out and I cant recognize the type of molecule
since there are 6 different type of mlecules in that system.
thanks.
I know I'm still a bit lost as to what the problem is. You've conducted a
simulation, but
Dear all,
I would like to make a series of simulation with drug in lipid with increasing
concentration.
In order to combine two files and delete overlapping lipid molecules from the
ligand, I am using genbox option (genbox -cp drg.pdb -cs lipid.pdb -o
lipid2.pdb).
For more than one drug,
serdar durdagi wrote:
Dear all,
I would like to make a series of simulation with drug in lipid with
increasing concentration.
In order to combine two files and delete overlapping lipid molecules
from the ligand, I am using genbox option (genbox -cp drg.pdb -cs
lipid.pdb -o lipid2.pdb).
Dear users,
I am trying to simulate electroosmotic flow using GROMACS.
The liquid is water and I am trying to find the dielectric constant of
water. I am just getting a value of dielectric constant of 10. i am
expecting 80 for water. I am attaching my mdp . I would be grateful if
Hi users
I am modeling the aggregation of an amphoteric molecule in aqueous media, and
to analyze the trajectories,
I want to plot the number of monomers in the aggregates vs time and the kind of
groups because in some trajectories i have dimers and monomers, or dimers and
trimers and so on
Vitaly,
What I am trying to do is simulate a CNT in air and measure temperatures. I
have found a paper that uses Morse potentials for Nitrogen and Oxygen. I am
not familiar with how to use Morse potentials. Can I use morse potentials
for air and Lennard-Jones for the CNT at the same time? If so,
I am afraid you can forget that your simulation is complete.
Make new .top and .gro and start it from the very beginning.
huan wrote:
Dear all gmx-users and developers,
The simulation has been carried out and I cant recognize the type of
molecule since there are 6 different type of
Very interesting... At present I work with CNTs as well. Although
together with non-aqueous liquids and electrolyte solutions.
Yes, you can use morse terms for gases, just consult the Chapter 5 of
the manual how to make your own parameter file (or modify the existing
one).
2008/8/13 Andy
There is no need to use x2top to make so primitive topology. It is
much easier to type it by hand. But even if you decided to do it you
should firstly add the 1-bonded nitrogen (and I guess, the same for
oxygen further) atom to ffgmx.n2t file.
If I were you I would make the own FF not to depend
Hi users
I am modeling the aggregation of an amphoteric molecule in aqueous media, and
to analyze the trajectories,
I want to plot the number of monomers in the aggregates vs time and the kind
of groups because in some trajectories i have dimers and monomers, or dimers
and trimers and so
Dear mark and justin
hi,thank you for your advices.
I want to make simulation peptide in 30%tfe.I get tfe.pdb and take
tfe.gro from prodrug program.I make solvatedtfe.gro and the other
solvatedspc.gro.then I make 30mol tfe and 70 spc in a file by
hands.and then run genbox -f .cs 3tfe70spc.gro
35 matches
Mail list logo
