RE: [gmx-users] eigenvectors with nan values

2012-08-21 Thread Joaquim Rui de Castro Rodrigues
-users] eigenvectors with nan values On 20/08/2012 4:34 AM, Joaquim Rui de Castro Rodrigues wrote: > Dear Gromacs users, > > I'm having problems with g_covar because sometimes it produces eigenvectors > with nan values. This is related with a previous post > (http://lists.groma

Re: [gmx-users] eigenvectors with nan values

2012-08-19 Thread Mark Abraham
On 20/08/2012 4:34 AM, Joaquim Rui de Castro Rodrigues wrote: Dear Gromacs users, I'm having problems with g_covar because sometimes it produces eigenvectors with nan values. This is related with a previous post (http://lists.gromacs.org/pipermail/gmx-users/2012-July/073492.html). I checked th

[gmx-users] eigenvectors with nan values

2012-08-19 Thread Joaquim Rui de Castro Rodrigues
Dear Gromacs users, I'm having problems with g_covar because sometimes it produces eigenvectors with nan values. This is related with a previous post (http://lists.gromacs.org/pipermail/gmx-users/2012-July/073492.html). I checked the integrity of my xtc and tpr/pdb input files, and everything se

Re: [gmx-users] Eigenvectors

2011-01-27 Thread Tsjerk Wassenaar
Hi Yao, They are. But if you really want to check, convert the eigenvectors to a human readable format (.gro/.g96) and calculate inner products :) Cheers, Tsjerk On Fri, Jan 28, 2011 at 2:43 AM, Yao Yao wrote: > > > >> Hi Gmxers, >> >> I am just wondering if the eigenvectors in gromacs are >>

[gmx-users] Eigenvectors

2011-01-27 Thread Yao Yao
> Hi Gmxers, > > I am just wondering if the eigenvectors in gromacs are > normalized or not. > thanks, > > Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Maili

[gmx-users] Eigenvectors

2011-01-27 Thread Yao Yao
Hi Gmxers, I am just wondering if the eigenvectors in gromacs are normalized or not, and how to check that after the normal mode analysis/ thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

[gmx-users] Eigenvectors

2011-01-27 Thread Yao Yao
Hi Gmxers, I am just wondering if the eigenvectors in gromacs are normalized or not, and how to check that after the normal mode analysis/ thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

[gmx-users] eigenvectors in readable format

2010-10-15 Thread Ramachandran G
Hi gmx users: I did normal mode analysis and got the hessian.mtx . Using the command g_nmeig_d on the hessian.mtx i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr. I need the complete eigenvector in the readable format. How i can get it? Thank you. with regards, Rama -- Postdoctoral Rese

Re: [gmx-users] eigenvectors in eigenvec.trr file

2007-05-09 Thread Tsjerk Wassenaar
Hi Sunita, Didn't you have a t=-1 for the reference structure? At least I think that the reference structure will account for the additional vector. Cheers, Tsjerk On 5/9/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: Dear Users, Covarience analysis is performed on Calpha atoms of the pept

[gmx-users] eigenvectors in eigenvec.trr file

2007-05-09 Thread sunita
Dear Users, Covarience analysis is performed on Calpha atoms of the peptide simulation. g_covar writes eigenvectors to a trajectory file (eigenvec.trr).I converted this file into readable format by using gmxdump.It gives the eigenvectors with eigenvector number as timestamp. t=0 corresponds to ave