Re: [gmx-users] free energy calculation

2008-04-23 Thread Maik Goette
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

Re: [gmx-users] trjconv error

2008-04-23 Thread Ragothaman Yennamalli
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

Re: [gmx-users] grompp error, invalid line in .gro file [SOLVED]

2008-04-23 Thread Andreas Kring
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 _

[gmx-users] couette flow

2008-04-23 Thread Matthew Schneemilch
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 __

FW: [gmx-users] couette flow

2008-04-23 Thread Berk Hess
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

Re: [gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

2008-04-23 Thread Vasilii Artyukhov
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

[gmx-users] urgent question

2008-04-23 Thread Prettl Zsolt
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 ___

Re: [gmx-users] urgent question

2008-04-23 Thread Ran Friedman
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

Re: [gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

2008-04-23 Thread Marc F. Lensink
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

Re: [gmx-users] urgent question

2008-04-23 Thread Justin A. Lemkul
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

RE: [gmx-users] couette flow

2008-04-23 Thread Berk Hess
> 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:

RE: [gmx-users] couette flow

2008-04-23 Thread Matthew Schneemilch
--- 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] >

[gmx-users] Re: Fatal error:couldnt write energies

2008-04-23 Thread sudheer babu
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

Re: [gmx-users] Re: Fatal error:couldnt write energies

2008-04-23 Thread David van der Spoel
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

[gmx-users] Fatal error:couldn't write energies

2008-04-23 Thread sudheer babu
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'

Re: [gmx-users] urgent question

2008-04-23 Thread Prettl Zsolt
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

[gmx-users] Fatalerror: Couldnt write energies

2008-04-23 Thread sudheer babu
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

RE: [gmx-users] couette flow

2008-04-23 Thread Berk Hess
> 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 > >

Re: [gmx-users] Entropy correction in PMF

2008-04-23 Thread Ángel Piñeiro
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

[gmx-users] Installation problem on Mac OS-X

2008-04-23 Thread Zuowei Wang
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

[gmx-users] Installation problem on Mac OS X

2008-04-23 Thread Zuowei Wang
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

[gmx-users] x2top error in CNT simulation on Gromacs 3.3.3

2008-04-23 Thread Hero
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

[gmx-users] Entropy correction in PMF

2008-04-23 Thread chris . neale
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

RE: [gmx-users] x2top error in CNT simulation on Gromacs 3.3.3

2008-04-23 Thread Christopher Stiles
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).