[gmx-developers] g_rmsf problem

[Anton Feenstra]

TAPO (Thomas Agersten Poulsen) wrote:
> 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.

Is this a dimer? Then, the PBC may be bugging you. Try 'trjconv -nojump' to
keep the monomers together, provided they were together in the beginning.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
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|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Costello)                                             |
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