AMBER Archive (2005)

Subject: Re: AMBER: a bimolecular reaction

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Wed Apr 13 2005 - 13:08:03 CDT

I don't know how to do that yet. Do you have some references or
tutorials? Thanks.

Eric

On 4/12/05, Yong Duan <duany_at_albert.genomecenter.ucdavis.edu> wrote:
>
> Can you grow/shrink instead?
>
> yong
>
> On Tue, 12 Apr 2005, Eric Hu wrote:
>
> > Thank you, Yong. The force parameters (bond, angle and etc) change
> > coupled with atom type changes. Since the two molecules eventually
> > become one, the CX---OX distance decreases to a normal C-OS distance.
> > The bond energy jumps to very high at the beginning of the vdw
> > perturbation and remains throughout the simulation, which makes me
> > think that TI is not very suitable for bond making process. Here is a
> > summary of the input and out files.
> >
> > Eric
> >
> > &cntrl
> > ntr=0,
> > nstlim =100000, nscm=2000, ntave=5000,
> > ntx=5, irest=1, ntb=0, 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 = 100, ntwx=1000,
> > icfe=1, klambda=6, clambda=0.05,
> > cut=999,
> > /
> >
> > |===============================================================================
> >
> > A V E R A G E S O V E R 50000 S T E P S
> >
> >
> > NSTEP = 100000 TIME(PS) = 120.000 TEMP(K) = 319.75 PRESS = 0.0
> > Etot = 1891.4011 EKtot = 35.9003 EPtot = 1855.5008
> > BOND = 1746.5250 ANGLE = 40.3842 DIHED = 58.1878
> > 1-4 NB = 15.0713 1-4 EEL = 0.0000 VDWAALS = -4.6675
> > EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
> > DV/DL = 19685.1423
> > ------------------------------------------------------------------------------
> >
> >
>
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