AMBER Archive (2002)

Subject: pressure variation coupled with taup value

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Oct 14 2002 - 04:36:42 CDT

Dear Amber users,
   I have several trajectories of an RNA-protein complex. All of them
are aroud 3 ns. One of them I have run with taup=0.2 while the others
with taup=2.0. The pressure is varying much more when taup=2.0 (I would
expect that.....correct me if I am wrong). The averages are a bit
different ...with a taup=0.2 I always get an average of 1.0 over 250 ps
while with taup=2.0 sometime I get 1.0 but other times I get 1.6 or 0.8.
  Now the question is: Knowing that taup=2.0 is more appropiate value
for dynamics runs and taup=0.2 for eq. runs how can I decide that the
pressure variation is within the acceptable limits....on the web it is
said that is satisfactory if most of values are within (-100; 100)
interval but what about being on the edge of this criterion? Is there a
way to judge if the variation of pressure is within acceptable limits?
  Thanks a lot for any answers,
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