AMBER Archive (2007)

Subject: Re: AMBER: Thermodynamic Integration with Explicit Solvent

From: David A. Case (case_at_scripps.edu)
Date: Tue Oct 09 2007 - 21:36:38 CDT

On Tue, Oct 09, 2007, Scott Pendley wrote:
>
> I have had a long history of using thermodynamic integration under AMBER 7
> using parmtops and perturbed parmtops. I have read through Ross' AMBER 9
> tutorial and I am trying to modify his implicit solvent tutorial to handle
> my explicit solvent needs but I am having trouble getting it to work.
>
> First I attempted to using an TI input that worked well for me before with
> AMBER 7
>
> &cntrl
> ntr=0,
> nstlim=3000000, 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, klambda=6,
> icfe=1, clambda=0.043882786,
> cut=9.0,
> /
>
> This unfortunately, led to errors with values exceeding the vmax.

You don't say very much about what else you did. For amber 9 you need two
prmtop files, one for each state. The first thing to do is to make sure that
each end state works well on its own (with no TI, icfe=0). Then, take a short
TI run but with lambda=0.0, and make sure you get exactly same result as for
the non-TI run. Ditto for lambda=1.0. Since you have klambda=6, I am
assuming you have dummy atoms: make sure the dummy atoms only exist in the
lambda=1.0 case (not in lambda=0.0). Be sure to follow the warnings in the
manual about having to be careful with SHAKE: you might want to try a short
run turning SHAKE off if you think that this might be a cause of the problem.

...dac

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