AMBER Archive (2004)

Subject: AMBER: pmf calculation using gibbs

From: Myunggi Yi (my02c_at_fsu.edu)
Date: Wed Feb 25 2004 - 10:47:25 CST

Hi, all.

In order to learn the gibbs program, I made two methanes in water, following a
paper.
I'd like to vary the distance between two carbon atoms
from 8 to 2.5 angstroms.
The following is the input file

FEP two methanes PMF
&cntrl

ntx=1,
ntb=2,
ntp=1,
ntt=5,

dt=0.001,

nstlim=20000,
nstmeq=5000,
nstmul=15000,
temp0=300.0,
ntc=2,
ntf=2,

ncorc=1,

cut=9.0,
intprt=0,

ntpr=50,
ntwx=50,
ntwe=50,

nrun=51,
almda=1.0,
almdel=0.02,
isldyn=-3,
ielper=0,
intr=1,
scnb=2.0, scee=1.2,
&end
    1 6 0 0 1 0 1 1.00000 0.00000
   5.00000 2.50000 5.00000 8.00000 0 0

I have calculated the distance from the trajactory.
I couldn't vary the distance from 8 angstroms.
What's problem?
Thanks and have a nice day. 

-- 
Best wishes,

Myunggi Yi
===========================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL. 32306

(850) 645-1334
http://www.csit.fsu.edu/~myunggi
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