[gmx-developers] g_rmsf problem

[TAPO (Thomas Agersten Poulsen)]

Hi Marco,

	I only wrote the protein and ions to the xtc-trajectory, but the
problem remains if I use the trr-trajectory for the g_rmsf calculation.

	It could look like what happens is that it writes the coordinates of
the C_alpha of the last frame, while keeping the coordinates of the starting
structure for all the rest. Does anybody know if that is the case?

Br
Thomas


-----Original Message-----
From: Marc Ceruso [mailto:mceruso at physbio.mssm.edu] 
Sent: 17. september 2003 19:28
To: 'gmx-developers at gromacs.org'
Subject: Re: [gmx-developers] g_rmsf problem

Hi-

Did you remove the PBC from your trajectory?

marco

-----Original Message-----
From: TAPO (Thomas Agersten Poulsen) 
Sent: 17. september 2003 16:18
To: 'gmx-developers at gromacs.org'
Subject: [gmx-developers] g_rmsf problem

Dear list,

	I have the following 2 problems using g_rmsf -oq to put RMDs of
C_alphas as B-factors in a PBD file:

1) On a 10ns trajectory the C_alpha atoms are displaced right out of the
box! This happens when using -b 0 -e 10000 or -b 0 -e 9000, but not using -b
0 -e 1000 or -b 0 -e 2000. 

2) The -q some.pdb -oq some_other does not seem to work. The original
B-factors in some.pdb are copied unchanged to some_other.pdb.

Hope somebody can help.
Best regards
Thomas


Thomas A. Poulsen (TAPo)
Novozymes A/S
1US.24
DK-2880 Bagsværd
+45 44 42 27 23

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-----Original Message-----
From: Marc Ceruso [mailto:mceruso at physbio.mssm.edu] 
Sent: 17. september 2003 19:28
To: 'gmx-developers at gromacs.org'
Subject: Re: [gmx-developers] g_rmsf problem