On 2010-03-09 20.01, Joe Joe wrote:
I also just tried on a different ALA and got the same problem.
can you please submit a bugzilla and upload files to reproduce the problem?
Ilya
On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe <[email protected]
<mailto:[email protected]>> wrote:
I am looking the the gmxdump output and everything seems consistent.
The only difference is that the numbering in the index file starts
at 1 whereas in the gmxdump the arrays are indexed starting at 0.
The coordinates look just fine.
Thanks,
Ilya
On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe <[email protected]
<mailto:[email protected]>> wrote:
I trjconv/ed xtc to pdb and loaded into vmd. The coordinates
looked fine.
I also
tpbconv/ed topol.tpr to topol_subset.tpr.
then I
editconf/ed topol_subset.tpr to gro and looked at the
coordinates. Index file matched and structure looked whole in vmd.
I will try the gmxdump
Thanks,
Ilya
On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel
<[email protected] <mailto:[email protected]>> wrote:
On 2010-03-09 19.16, Joe Joe wrote:
yep.
Have you gmxdump/ed the xtc to check the coordinates are right?
On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
<[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> wrote:
On 2010-03-09 19.09, Joe Joe wrote:
Hi I am trying to post process and xtc
trajectory using g_dist. I am
trying to calculate the CA-CB distance of an
Alanine residue but
I get
NAN in all the distance columns. It works for
the other residues
I've
tried (i.e. SER, VAL). I am using vsites in my
simulation and I
think it
may have some thing to do with the way gromacs
outputs the CB
positions
in the xtc file when the CB is part of the vsite
network. Any
thoughs?
Thanks,
Ilya
Are you sure your index file matches the xtc/tpr?
--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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