So, obviously, no one knows how to do that by g_lie. Most people here
compute free energies by TI.
Do some background reading and find out yourself how it works. Posting
mails twice or more won't help you
regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoret
Hi,
Thanks for the mail. Well, I am using a old version specifically, even though
newer versions are available. It is quite confusing since the same file is
being able to be read by other tools like gmxcheck. And it is while running by
gmxcheck that I get the Magic number error
Raghu
--- On We
Your formatting is incorrect.
The .gro format is a very old GROMOS fixed format (not free format).
See the manual for the details:
http://www.gromacs.org/documentation/reference/online/gro.html
Thanks a lot. Now everything works perfectly!
/Andreas
_
Hi,
Has anyone here used gromacs to simulate couette flows in slit pores? I can see
that it would be possible to use the pull code but I would like to be able to
run in parallel. Any tips before I begin modifying source code would be greatly
appreciated.
Cheers, Matt
__
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: RE: [gmx-users] couette flow
Date: Wed, 23 Apr 2008 11:57:17 +0200
> Date: Wed, 23 Apr 2008 02:34:49 -0700
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] couette flow
>
> Hi,
> Has anyone here used
Thanks Chris and Mark!
2008/4/21 Chris Neale <[EMAIL PROTECTED]>:
> I use tip4p/opls/berger combination and it works well for me. I have never
> used tip5p. I suggest that you build your membrane and run one control
> simulation (sounds like you would lean toward using spc for this) and then
> on
Hello!
I would like to use Cr3+ for my molecule modelling but I just could not find
a suitable one for Gromacs anywhere. If somebody has any suggestion, from
when can I download it, please write me ASAP, because it is very-very
important
Thanks in advance,
Zsolt
___
Hi,
You probably didn't find it because it's not so popular for simulations.
My suggestion is to look very carefully in the literature. Transition
metals are difficult to models, especially when you need to take into
account both their interactions with water and with proteins - see e.g.:
@Articl
On Wed, Apr 23, 2008 at 03:22:09PM +0400, Vasilii Artyukhov wrote:
>
> I'm afraid I have to use TIP5P; I _am_ looking at temperature dependent
> information, and also, I need a good description of hydration of small
> molecules I mentioned. These and other considerations make more or less
> every
Quoting Prettl Zsolt <[EMAIL PROTECTED]>:
> Hello!
>
> I would like to use Cr3+ for my molecule modelling but I just could not find
> a suitable one for Gromacs anywhere. If somebody has any suggestion, from
> when can I download it, please write me ASAP, because it is very-very
> important
S
> Date: Wed, 23 Apr 2008 05:29:26 -0700
> From: [EMAIL PROTECTED]
> Subject: RE: [gmx-users] couette flow
> To: [EMAIL PROTECTED]
>
>
>
>
> --- On Wed, 4/23/08, Berk Hess <[EMAIL PROTECTED]> wrote:
>
> > From: Berk Hess <[EMAIL PROTECTED]>
> > Subject: RE: [gmx-users] couette flow
> > To:
--- On Wed, 4/23/08, Berk Hess <[EMAIL PROTECTED]> wrote:
> From: Berk Hess <[EMAIL PROTECTED]>
> Subject: RE: [gmx-users] couette flow
> To: "Discussion list for GROMACS users"
> Date: Wednesday, April 23, 2008, 10:25 PM
> > Date: Wed, 23 Apr 2008 05:29:26 -0700
> > From: [EMAIL PROTECTED]
>
Thanks Mark for your reply, My system is neither full nor didnt do anything
with .edr file, I did same simulation again, same problem I got that stopped
my simulation and showed "fatal error: could not write energies"
Pls suggest me.
Thanks in advance
sudheer babu wrote:
>* HI gmx-users,
*>* Iam
sudheer babu wrote:
Thanks Mark for your reply, My system is neither full nor didnt do
anything with .edr file, I did same simulation again, same problem I got
that stopped my simulation and showed "fatal error: could not write
energies"
Pls suggest me.
Thanks in advance
is your edr file ex
Thanks David for your reply . No, the crashed .edr has only 216kb.
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don'
Thanks for everyone for the quick answers!
Zsolt
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscr
Thanks David for reply. No,.edr which crahsed contain 216kb.
sudheer babu wrote:
>* Thanks Mark for your reply, My system is neither full nor didnt do
*>* anything with .edr file, I did same simulation again, same problem I got
*>* that stopped my simulation and showed "fatal error: could not wri
> Date: Wed, 23 Apr 2008 06:56:32 -0700
> From: [EMAIL PROTECTED]
> Subject: RE: [gmx-users] couette flow
> To: gmx-users@gromacs.org
>
>
>
>
> --- On Wed, 4/23/08, Berk Hess <[EMAIL PROTECTED]> wrote:
>
> > From: Berk Hess <[EMAIL PROTECTED]>
> > Subject: RE: [gmx-users] couette flow
> >
I sent the attached message on last March 31 but I didn't get any
answer... may be the right people was not available at that time and
that is why I am trying again. I would thank a lot to have some more
detail about this paragraph in the gromacs manual (version 3.3, chapter
6, page 111):
“Whether
Dear All,
I am trying to install Gromacs-3.3.3 on a Power Mac G5 with the
system version of
Mac OS X 10.4.11 and kernel version of Darwin 8.11.0. After the
successful
installation of fftw-3.1.2 into a directory (using --prefix) of /
programs/fftw312/, the
installation of gromacs-3.3.3 faile
Dear All,
I am trying to install Gromacs-3.3.3 on a Power Mac G5 with the
system version of
Mac OS X 10.4.11 and kernel version of Darwin 8.11.0. After the
successful
installation of fftw-3.1.2 into a directory (using --prefix) of /
programs/fftw312/, the
installation of gromacs-3.3.3 faile
Dear All,
I am trying to simulate water flow in CNT and just followed the website:
http://cs86.com/CNSE/SWNT.htm
I did the following:
1. ffgmx.n2t
must change this files name to ffencadv.n2t and add the following 2 lines:
C C 1 C ; CNT Carbon with one bond
C C 2 C C ; CNT double bonded Carb
That sentence could definitely use some massaging. Try this:
Whether one needs to correct for this contribution depends on what the
pmf should represent. When one wants to pull a substrate into a protein,
this entropic term indeed contributes to the work to get the substrate
into the protein. Thi
Send a copy of your ffgmx.n2t, ffgmxbon.itp, and SWNT_6_6_144.pdb files
please, if the following does not work. Also I think that the information
updated in ffgmxbon.itp might be found in a different file with the 3.3.3
version (I think from looking at previous e-mails that it is
ffencadvbon.itp).
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