AMBER Archive (2006)

Subject: AMBER: Different results for TI calculation

From: Biswa Ranjan Meher (brmeher_at_iitg.ernet.in)
Date: Wed May 31 2006 - 02:25:13 CDT

Dear Dr. Case,
This mail is a continuation of my previous mail. I have read your tutorial
on thermodynamic integration (TI) and I was performing the same calculation (Tolune---> nothing) in
the tutorial given. I performed the charging free energy calculations for both in vaccum and in
water and got the results close to the tutorial. But unfortunately I got much different results
when performed for disappearing free energy calculation as compared to the tutorial.

For disappearing free energy calculation in water part I equilibrated the system for each individual
values of clambda and then run for the production for the same value of clambda. I used five values
of clambda from 0.05, 0.15,0.25, 0.35 and 0.45 with klambda =4. Here is my result which is far
different from the results of your tutorial.

DV/DL from my calculation :
13.2628, 4.1287, 1.3485, 0.0854, -0.0716 for values of clambda 0.05,
0.15, 0.25, 0.35 and 0.45 respectively.

DV/DL from tutorial:
22.0, 12.0, 6.0, 0.12 and -0.05 (approximately) of clambda 0.05,0.15,
  0.25, 0.35 and 0.45 respectively.

Here is an equilibration input file for a value of clambda = 0.05

neutralize toluene
&cntrl
ntr=0,
nstlim =20000,
nscm=2000, ntave=5000,
ntx=1, irest=0, ntb=2, ntpr=100,tempi=300.0, ig=974651,
ntp=1, taup=1.0,
dt=0.001, nrespa=1,ntt=1, temp0=300., tautp=2.0,
ntc=2, ntf=2, tol=0.000001,
ntwr=10000, ntwx=0,
icfe=1, clambda=0.05, klambda=4,
cut=9.0,
&end

Here is an production input file for a value of clambda=0.05

neutralize toluene
&cntrl
ntr=0,
nstlim =100000,
nscm=2000, ntave=5000,
ntx=7, irest=1, ntb=1,ntpr=100,
ntp=0, taup=2.0,
dt=0.001,nrespa=2,
ntt=0, temp0 = 300., tautp=2.0,
ntc=2,ntf=2, tol=0.000001,
ntwr = 10000, ntwx=0,
icfe=1,clambda=0.05, klambda=4,
cut=9.0,
&end

I am using the AMBER-8 version in a Linux system.
So can you please point out the reason of differnce in results and also the
mistake.

With regards
Biswa Ranajn Meher 

-- 
......................XXXXXXXXXXXXXXXXXX................................
Mr. Biswa ranjan Meher (Research Scholar)          Room:119
Dept. Of Biotechnology, IIT-Guwahati,              Siang Hostel
North Guwahati, Assam-781039                       IIT-Guwahati
Phone:0361-2582246(Lab)                            Phone:0361-2582766/7/8
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