AMBER Archive (2002)

Subject: ptraj problem

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Jun 24 2002 - 10:54:32 CDT

I am using ptraj to analyse some trajectories.
I have a script for calculating the atomic fluctuations:

#!/bin/csh -f

set fname=${1}

${AMBEREXE}/ptraj ../../${fname}.top << End

trajin ../../../${fname}_md00.mdcrd.Z
trajin ../../../${fname}_md01.mdcrd.Z
#trajin ../../${fname}_md02.mdcrd.gz
#trajout prot_rna_dyn_md.mdcrd

center :1-142 mass origin
image origin :1-142

atomicfluct out fluct_byatom.dat :126-142
atomicfluct out fluct_byres.dat :126-142 byres

go

End

exit

The problem is that for the same trajectory if I want to calculate also
some rmsd and I insert the lines:

rms first out rms.dat :1-142

rms first out rms_1.dat :126
rms first out rms_2.dat :127
rms first out rms_3.dat :128
rms first out rms_4.dat :129
rms first out rms_5.dat :130
rms first out rms_6.dat :131
rms first out rms_7.dat :132
rms first out rms_8.dat :133
rms first out rms_9.dat :134
rms first out rms_10.dat :135
rms first out rms_11.dat :136
rms first out rms_12.dat :137
rms first out rms_13.dat :138
rms first out rms_14.dat :139
rms first out rms_15.dat :140
rms first out rms_16.dat :141
rms first out rms_17.dat :142

just before the atomicfluct command I obtained completely different
results for the atomic flucuations. The question is why?
Thanks in advance for any kind of suggestions
vlad 

-- 
Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
Deparment: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de