AMBER Archive (2003)

Subject: RE: TAUP and density problem

From: case (case_at_scripps.edu)
Date: Sun Feb 16 2003 - 19:36:48 CST

>===== Original Message From yuan bo <yuanbous_at_yahoo.com> =====

>I also simulate one protein in nonaqueous solvent.

Which non-aqueous solvent? What is the density supposed to be?

>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.

You should look at the profile of the density (or volume) vs. time: does
it converge to the final value pretty quickly (over say 10-20 ps) and then
stay there?

>
>&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
>
The only thing I can see is that you probably should be using ntx=7 (not
5) if the previous runs were with constant P. Otherwise, you will be
starting over with you initial volume and density, rather than the one
from the end of the previous run.

Something certainly sounds wrong, but I can't tell what it is without
knowing more. As I suggested, be sure to look carefully for any funny
things with the density vs. time behavior. Be sure that the temperatures
and energies are stable as well.

...good luck...dac

==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================