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
Received on Mon Oct 14 2002 - 02:36:42 PDT
