[gmx-developers] g_rmsf problem

[Marco Ceruso]

Hi Thomas-
 I am not sure that I understand you completely...
My guess from what you described was that between 1.0 and 2.0ns your peptide
was still in the box
but after sometime it crossed the box boundaries. So before you analyze
the rmsf try to use trjconv -pbc whole -fit -center etc... to make your
peptide
whole again ,fit it to a reference and center it in the middle of the box
(optional),
then calculate the rmsf, rmsd...
otherwise you can use g_traj -com to follow the coordinates of the center of
mass of your peptide
in time (remmber the starting point is in the middle of the box,
i.e.box_length/2).
best
marco



-----Original Message-----
From: gmx-developers-admin at gromacs.org
[mailto:gmx-developers-admin at gromacs.org]On Behalf Of TAPO (Thomas
Agersten Poulsen)
Sent: Thursday, September 18, 2003 3:00 AM
To: 'gmx-developers at gromacs.org'
Subject: RE: [gmx-developers] g_rmsf problem


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

_______________________________________________
gmx-developers mailing list
gmx-developers at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-developers
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-developers-request at gromacs.org.

-----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


_______________________________________________
gmx-developers mailing list
gmx-developers at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-developers
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-developers-request at gromacs.org.