Dear Dr. Warren,
Thank you very much from your help.
Best Regards
Dina
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Dear GROMACS Specialists,
I have doubt about these error estimates for Rg and Rg(x,y,z). May I ask you to
say me why is the difference between them. for example for Rg is 0.0002 and for
others is 0.00x?!
And are my error estimates true?
Please help me.
You didn't reply the part where I told unless you're trying to have
some advantage...
-- Forwarded message --
From: Mark Abraham mark.abra...@anu.edu.au
Date: 2012/5/6
Subject: Re: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?
To: Discussion list for GROMACS
First i had simulation of the protein alone in united atom gromacs force
field by -ff gmx in pdb2gmx
now i am unable to run the protein-ligand complex for the same protein with
a ligand,
it says the following error due to itp file generated from PRODRG,
if i change the force field its says atom
On Mon, May 7, 2012 at 5:11 PM, Sarath Kumar Baskaran
bskumar.t...@gmail.com wrote:
First i had simulation of the protein alone in united atom gromacs force
field by -ff gmx in pdb2gmx
now i am unable to run the protein-ligand complex for the same protein
with a ligand,
it says the
On 5/6/12 11:11 PM, Debayan Chakraborty wrote:
Dear Justin,
The Jorgensen group have already published results for
aniline and DMA using the OPLS-AA parameters. I am using the charges from their
publication ( R. Rizzo and W.L.Jorgensen, J.Am.Chem.Soc., 1994, 121,
On 5/7/12 1:01 AM, Anirban Ghosh wrote:
On Mon, May 7, 2012 at 10:17 AM, Bala S think_bey...@aol.com
mailto:think_bey...@aol.com wrote:
Justin and Anirban,
I have another query on membrane simulation following your tutorials.
How do I insert only a part of protein into the
On 5/7/12 7:41 AM, Sarath Kumar Baskaran wrote:
First i had simulation of the protein alone in united atom gromacs force field
by -ff gmx in pdb2gmx
now i am unable to run the protein-ligand complex for the same protein with a
ligand,
it says the following error due to itp file generated
Dear Marcelo,
I think you need to calm down. You are using a very nice piece of free code
which has in excellent documentation as well as being open source.
If you are using a piece of software in a non-standard way it stands to reason
that it might not be documented. When this occurs in my
Hi,
Please send requests for help to the gmx-users mailing list. I (and most
others there) are not available as private tutors.
Contrary to your assertion below, I've never run any simulations on
cytochrome P450. You probably need to name your iron atom more suitably
for your force field to
Hi,
g_current calculates the (ionic) current in the output file specified by the
-o switch (by default, current.xvg). Specifically, each component (x, y,
and z) of the current is computed and printed.
My question is, is the current that is computed the current of atoms (which
each have partial
Dear Gromacs users,
I work with Gromacs in Linux, I want prepare a copy of snapshots by ngmx with
jpg or pdf format or whatever that be open in Windows.
May I ask you to help me,Please?
Best Regards
Sara
--
gmx-users mailing listgmx-users@gromacs.org
On 5/7/12 1:50 PM, mohammad agha wrote:
Dear Gromacs users,
I work with Gromacs in Linux, I want prepare a copy of snapshots by ngmx with
jpg or pdf format or whatever that be open in Windows.
May I ask you to help me,Please?
ngmx is a very simple viewing program. There are far better
Hi
So you think that I should edit something in ffbonded.itp? The parameters that
I would write by hand in the topology should be supplemented in the
ffbonded.itp?
I don't really know what I have to do concretely, to fix this problem.
Greetings
Lara
- Ursprüngliche Message -
On 5/7/12 2:54 PM, Lara Bunte wrote:
Hi
So you think that I should edit something in ffbonded.itp? The parameters that
I would write by hand in the topology should be supplemented in the
ffbonded.itp?
I don't really know what I have to do concretely, to fix this problem.
If the
Thank you for your reply, Mark,
On Sat, May 5, 2012 at 7:06 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
Fundamentally, pdb2gmx is built for fine-grained force fields. I'd have
supposed Martini has some kind of builder program other than pdb2gmx, for
this kind of reason, but I have no idea
Dear users:
I am writing my methods section for a simulation in which I used -vsites
hydrogens and I want to ensure that I have the reference correct. The gmx-4.5.4
manual does not list a reference that I could see for this usage by searching
vsites.
Is this the correct reference:
Feenstra,
On Wed, May 2, 2012 at 11:51 AM, melichercik melicher...@nh.cas.cz wrote:
Hi people,
we plan to buy some computer mostly for gromacs, so I want to ask you for
some hints. I'd tried to do some research, but no success. :(
Have someone ever compared AMD Bulldozer and Sandy/Ivy Bridge
On Wed, May 2, 2012 at 12:17 PM, Thomas Evangelidis teva...@gmail.comwrote:
For CPU performance comparison look at:
www.spec.org/cpu2006/results
for each CPU look at the statistics for floating point operations, namely
for SPECfp_base2006 score for the programs of interest (GAMESS, GROMACS,
On Wed, May 2, 2012 at 5:44 PM, Peter C. Lai p...@uab.edu wrote:
When considering compute hardware today, you're gonna have to shop like a
gamer. A rig that can get high Battlefield 3 or Arma 2/3 framerates should
also be able to get you some nice ns/day.
(To a great extent) wong! While many
On Wed, May 2, 2012 at 6:13 PM, Mirco Wahab
mirco.wa...@chemie.tu-freiberg.de wrote:
Hello Peter,
Am 02.05.2012 17:44, schrieb Peter C. Lai:
You can wait for ivy bridge, then stick some Kepler GPUs (nvidia gtx
680) in it. That should max the performance. asm is pretty much stagnant
for
On Fri, May 4, 2012 at 8:58 PM, Oliver Stueker ostue...@gmail.com wrote:
Hi all,
This week Nvidia has also announced the GeForce GTX 690 with two
Kepler Chips [1].
That will make a total of 3072 CUDA cores @ 915MHz to 1019MHz and will
perform like two GTX 680s in SLI mode [2], but more
On Fri, May 4, 2012 at 9:20 PM, Roland Schulz rol...@utk.edu wrote:
On Wed, Apr 25, 2012 at 9:38 AM, Szilárd Páll szilard.p...@cbr.su.se
wrote:
On Wed, Apr 25, 2012 at 11:43 AM, SebastianWaltz
sebastian.wa...@physik.uni-freiburg.de wrote:
Dear all,
will the new version 4.6 work
On 8/05/2012 5:19 AM, Elton Carvalho wrote:
Thank you for your reply, Mark,
On Sat, May 5, 2012 at 7:06 AM, Mark Abrahammark.abra...@anu.edu.au wrote:
Fundamentally, pdb2gmx is built for fine-grained force fields. I'd have
supposed Martini has some kind of builder program other than pdb2gmx,
Dear,
Could anyone please let me know, in Gromacs analysis is there any way to
get the local pressure (along z-axis of the box)?
Thanks a lot!
Cuong Nguyen
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Dear Justin,
Thank you very much from your reply.
I installed VMD on my system before but when I type vmd in terminal, the basic
page of VMD flash and disappear!!! Because of my system was sensitive So, I
decided work by ngmx. Can you help me about this problem, Please?
Best Regards
Sara
On 5/7/12 9:42 PM, mohammad agha wrote:
Dear Justin,
Thank you very much from your reply.
I installed VMD on my system before but when I type vmd in terminal, the basic
page of VMD flash and disappear!!! Because of my system was sensitive So, I
decided work by ngmx. Can you help me about this
Dear Justin,
Thank you very much from your response.
Best Regards
Sara
From: Justin A. Lemkul jalem...@vt.edu
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Tuesday, May 8, 2012 6:15 AM
Subject: Re:
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