AMBER Archive (2005)

Subject: Re: AMBER: a bimolecular reaction

From: Yong Duan (duany_at_albert.genomecenter.ucdavis.edu)
Date: Tue Apr 12 2005 - 19:22:51 CDT

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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