[gmx-users] make_edi, g_covar -nofit

[vijaya subramanian]

Hi Carsten,
I downloaded the clone and patches, copied make_edi.c to /src/tools and
recompiled gromacs-4.0.7 as suggested by Mark.  Now make_edi works with
.trr files generated using either g_covar -nofit or -fit but the .edi files generated
now have only the average structure recorded under both xref and xav.

For example:#NREF, XREF 
 172 
1  0.989554  -2.893834  0.667306
2  0.825675  -2.659700  0.913271
3  0.760027  -2.801672  1.259611
4  0.500538  -2.530900  1.332710
5  0.292291  -2.620316  1.021137
6  -0.021384  -2.793121  1.143848
7  -0.302607  -2.782386  0.888191
8  -0.190402  -2.495389  0.666387
9  -0.237132  -2.500305  0.290461
.....
#NAV, XAV 
 172 
1  0.989554  -2.893834  0.667306
2  0.825675  -2.659700  0.913271
3  0.760027  -2.801672  1.259611
4  0.500538  -2.530900  1.332710
5  0.292291  -2.620316  1.021137
6  -0.021384  -2.793121  1.143848
7  -0.302607  -2.782386  0.888191
8  -0.190402  -2.495389  0.666387
9  -0.237132  -2.500305  0.290461
.....

If I am not mistaken, the reference structure is needed for the ED sampling.  This could be obtained from
the structure file 
make_edi -s ref.gro

Thanks for your help.
Vijaya


From: ckutzne at gwdg.de
Subject: Re: [gmx-users] make_edi, g_covar -nofit
Date: Wed, 5 May 2010 17:10:03 +0200
To: gmx-users at gromacs.org



Hi,
On May 5, 2010, at 5:01 PM, vijaya subramanian wrote:Hi
No, the original gromacs-4.0.7 installation was not a clone from the repository.  
So I uninstall that, and install the clone after getting the patches?
This would be convenient since for more bug fixes you would then just need todo a 'git pull' and a recompile. Alternatively, you can, as Mark suggested, copy the make_edi.c program from thegit gromacs directory to the corresponding location in your 4.0.7 directory andthen issue a 'make' and 'make install' again.
Carsten
Thanks
Vijaya


From: ckutzne at gwdg.de
Subject: Re: [gmx-users] make_edi, g_covar -nofit
Date: Wed, 5 May 2010 09:49:22 +0200
To: gmx-users at gromacs.org

On May 4, 2010, at 10:56 PM, vijaya subramanian wrote:Hi Carsten 
A couple of quick questions:
I already have gromacs-4.0.7 downloaded from the gromacs website.  I found that I couldn't 
use git checkout --track -b release-4-0-patches origin/release-4-0-patches to get the patches.
fatal: Not a git repository
Do I have to uninstall gromacs-4.0.7 and re-install gromacs obtained from the git site as below,
then install gromacs again?

Hi,
if the git clone command worked, then the git checkout --track should also work.Maybe you forgot to change into the gromacs directory that was produced by thefirst command? You have to do the checkout --track in the directory where a.git subdir is present.
git clone git://git.gromacs.org/gromacs.git
cd gromacs
git checkout --track -b release-4-0-patches origin/release-4-0-patches

Carsten
--Dr. Carsten KutznerMax Planck Institute for Biophysical ChemistryTheoretical and Computational BiophysicsAm Fassberg 11, 37077 Goettingen, GermanyTel. +49-551-2012313, Fax: +49-551-2012302http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne


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--Dr. Carsten KutznerMax Planck Institute for Biophysical ChemistryTheoretical and Computational BiophysicsAm Fassberg 11, 37077 Goettingen, GermanyTel. +49-551-2012313, Fax: +49-551-2012302http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne



 		 	   		  
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