AMBER Archive (2003)

Subject: TAUP and density problem

From: yuan bo (yuanbous_at_yahoo.com)
Date: Sun Feb 16 2003 - 03:29:34 CST

Dear all
I also simulate one protein in nonaqueous solvent.
When I use NTC=3,NTF=3,TAUP=0.2 in NPT equilibration,
the density would come to the equilibration(about
0.78g/cm3) about over 100ps. But when I select another
condition to NPT equilibration:NTC=2,NTF=2, I have to
set taup larger value than 1.0ps ( recommanded 1.0-5.0
when NPT>0 in manual), because the equilibration would
results in ewald bomd when I set taup < 1.0ps. But
density is not easy to equilibrate compared to the
condition of NTC=3 and TAUP=0.2. When I set
taup=2.0,the density just come to 0.72 after 400ps NPT
equilibration ( while density is equilibrated to be
about 0.79 over 100ps in NTC=3 and taup=0.2). so in
order to quikely converge density, I do additionally
200ps taup=1.0 NPT equilibration after 400ps
equilibration with taup=2.0. In this condition, the
density first rise to 0.92 and then gradually drop to
0.85, but the density still don't come to
equilibration ( total equilibration time is up to
600ps). so I can't do production MD.
   The problem is: Would different taup values lead to
different density for the system or larger taup value
is and slower the density converge to equilibration?
>From my simulation, it present that larger the taup
and slower the box size shrink in NPT equilibration.
Could anybody give me some suggestion and help? My
system have about 16000 atoms and input file as
followes:

&cntrl
imin=0,ntb=2, ntp=1, cut=12.0, ntwx=200, ntwe=200,
nstlim=100000, ntc=2, dt=0.001, ntt=1, ntx=5,
 irest=1, ntpr=200,ntf=2,taup=2.0( or 1.0)
&end

Thanks
yb
 
  

__________________________________________________
Do you Yahoo!?
Yahoo! Shopping - Send Flowers for Valentine's Day
http://shopping.yahoo.com