On 1/27/10 7:49 AM, swa...@ncbs.res.in wrote:
Dear Dr. Spoel,
I am garduate student in National Centre for Biological
Sciences(NCBS-TIFR), India. I am willing to do Locally Enhanced
Sampling(LES) in one my research project.I saw few webpages on LES using
GROMACS but not able to find any proper d
On 27/01/10 15:58, vivek sharma wrote:
Hi Dallas,
I am trying to run MD simulation over a docked complex (protein+ligand),
to confirm their dynamic stability in water media.
For the same I am using PRODRG server to generate topologies for ligand
molecule as gromacs can generate topology for 20 st
Hi Vivek,
Either
1. Use the original ligand coordinates with the PRODRG topology
or
2. Fit the structure obtained from PRODRG to the original structure
Cheers,
Tsjerk
On Wed, Jan 27, 2010 at 5:58 AM, vivek sharma
wrote:
> Hi Dallas,
> I am trying to run MD simulation over a docked complex (
Hi Dallas,
I am trying to run MD simulation over a docked complex (protein+ligand), to
confirm their dynamic stability in water media.
For the same I am using PRODRG server to generate topologies for ligand
molecule as gromacs can generate topology for 20 standard residues. As
mentioned in tutorial
Dear all:
These days, I am trying to pull a slab of griphene moving along the Z direction
at a constant speed. The slab of griphene contains 700 atoms. After several
times of E-mail communication with the Gromacs users, the simulation can
run. However, the run didn't produce the results which I
On 27/01/10 15:11, rituraj purohit wrote:
I want get rmsd deviation between NMR structure and the simulated
result, but i am getting following error in following command.
g_rms -s em.tpr -f md.trr -o rsmd_Calpha.xvg
WARNING: topology has 50772 atoms, whereas trajectory has 22899
---
I want get rmsd deviation between NMR structure and the simulated result,
but i am getting following error in following command.
g_rms -s em.tpr -f md.trr -o rsmd_Calpha.xvg
WARNING: topology has 50772 atoms, whereas trajectory has 22899
---
Pro
Hello everybody,
I tried to install gromacs 4.0.7 + openMM on Fedora core 10 x86_64, but I
had lots of problems with that.
I typed the configure options below to obtain a Makefile:
$ ./configure --enable-shared --prefix=/opt/gromacs_openmm
CPPFLAGS="-I/opt/openmm/include/openmm/ -I/opt/openmm/i
- Original Message -
From: Yanmei Song
Date: Wednesday, January 27, 2010 10:58
Subject: Re: [gmx-users] Potential Energy
To: jalem...@vt.edu, Discussion list for GROMACS users
> Dear Justin:
>
> I finally figure out that the problem comes from the Coulomb 1-4 interactions
> defined b
Dear Justin:
I finally figure out that the problem comes from the Coulomb 1-4
interactions defined by [pairs] part. When I remove this parts, the energy
minimization ends with a big negative number. Thanks for your help.
On Tue, Jan 26, 2010 at 4:24 PM, Justin A. Lemkul wrote:
>
>
> Yanmei Song
Yanmei Song wrote:
Dear Justin:
Sorry, that itp is the original one generated by PRODRG. Also I have
modified it based on a optimized force field of the molecule. (See
attached file and the literature of the force field). But still the
potential energy is positively 1e2 and why the system c
Dear gromacs users:
I have a couple of questions:
While doing auto correlation function under what condition i need
to use polynomials?
Apart from the fit functions existing in the gromacs how can i use
different functions like
stretched exponential in the form P(t)=ex
nce, for systems in such size, the
potential energy
is usually a big negative number? Does this mean that my force field
parameter or molecule structure have problems? Thanks in advance!
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Ariz
-0700
> From: Yanmei Song
> Subject: [gmx-users] Potential Energy
> To: Discussion list for GROMACS users
> Message-ID:
>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Users:
>
> I am in the process of setting up a new system. I have a 8.
Yanmei Song wrote:
Dear Justin:
Thanks for your response. I got my force field parameters from PRODRG.
The system run well and I got a very reasonable density profile. Just
can not figure out what is the problem. I attached my itp file and gro
file. Would you please help me check what is th
Yanmei Song wrote:
Dear Users:
I am in the process of setting up a new system. I have a 8.0*8.0*8.0
nm3 system which include 27800 molecules. When the system approach
equilibrium, I found the potential energy is +3e5 (big positive number).
Is this normal? Since based on my experience, for
atal error:
The solvent group SOL is not continuous: index[9]=1732, index[10]=1747
---
"Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is." (Jackie
Brown)
*I do not know the reason,the number of residues in top f
Dear Users:
I am in the process of setting up a new system. I have a 8.0*8.0*8.0 nm3
system which include 27800 molecules. When the system approach equilibrium,
I found the potential energy is +3e5 (big positive number). Is this normal?
Since based on my experience, for systems in such size, the
Miguel Quiliano Meza wrote:
*Hi everyone.
I have a problem when I try to run GENION, GROMACS says:
*
WARNING: turning of free energy, will use lambda=0
Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
Using a coulomb cut-off of 0.9 nm
Will try to add 0 Na ions and 15 NA+ ions.
*Hi everyone.
I have a problem when I try to run GENION, GROMACS says:
*
WARNING: turning of free energy, will use lambda=0
Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
Using a coulomb cut-off of 0.9 nm
Will try to add 0 Na ions and 15 NA+ ions.
Select a continuous group of so
So, what EXACTLY are you doing?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the o
Stephane Abel wrote:
Thank you Roland for your response
I have effectively downloaded from the
http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version
of gmx Unfortunately, the unpacked directory does not contain a
configure file, I have only an configure.ac.
So my question
Thank you Roland for your response
I have effectively downloaded from the
http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version
of gmx Unfortunately, the unpacked directory does not contain a
configure file, I have only an configure.ac.
So my question is: how to obtain a ful
Thank you .
Carla
On Tue, Jan 26, 2010 at 11:53 AM, Carsten Kutzner wrote:
>
> On Jan 26, 2010, at 11:48 AM, Carla Jamous wrote:
>
> > Hi everyone,
> >
> > Please I'm having a problem with mdrun:
> > If I type:
> > mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g
> test.lo
On Jan 26, 2010, at 11:48 AM, Carla Jamous wrote:
> Hi everyone,
>
> Please I'm having a problem with mdrun:
> If I type:
> mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g
> test.log
>
> I never get the .xtc file. Can anyone tell me why & what can I do to have an
> .x
Hi everyone,
Please I'm having a problem with mdrun:
If I type:
mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g
test.log
I never get the .xtc file. Can anyone tell me why & what can I do to have an
.xtc file?
Thank you
Carla
--
gmx-users mailing listgmx-users@gromac
I wish G96 force fields had a similar website with so much useful
information.
It would be good if authors posted anything on the forum cause it's
completely empty right now.
2010/1/26 XAvier Periole
>
> Dears,
>
> the MARTINI CG force field web site has been remodeled.
>
> It now includes FAQs,
Dears,
the MARTINI CG force field web site has been remodeled.
It now includes FAQs, tutorials, a forum and much more ...
http://md.chem.rug.nl/cgmartini
Enjoy.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear all,
We are proud to announce a CECAM tutorial on PLUMED.
PLUMED is an open source plugin for free-energy calculations in
molecular systems that can be interfaced, through a simple patch
procedure, with some of the most popular classical molecular dynamics
codes, including AMBER, GROMACS, NA
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