AMBER Archive (2006)

Subject: Re: AMBER: TI-FEP : strange result for different clambda values

From: David Mobley (dmobley_at_gmail.com)
Date: Fri Sep 22 2006 - 11:38:19 CDT

Biswa,

You could of course adjust your lambda spacing to have more lambda
values where dV/dlambda is large (the important regions) and fewer
where it is small...

David

On 9/22/06, Biswa Ranjan Meher <brmeher_at_iitg.ernet.in> wrote:
>
> Dear AMBER users,
> For my protein-drug system: we are doing the free energy perturbations in a
> transformation of ILE ---> VAL using the TI method. We used 14 windows of
> clambda value as 0.05, 0.15, 0.25........0.85 and 0.90, 0.92.....0.98 with
> klambda = 6, as per the AMBER tutorial for tolune-->nothing. But
> strange thing in the result is that, in the last windows of clambda value
> 0.90 to 0.98 we are getting the DV/DL almost zero difference. The
> different clambda values and there respective DV/DL values we found are as
> follows:
>
> clambda DV/DL
> 0.05 50.4736
> 0.15 25.9430
> 0.25 12.2901
> 0.35 5.2432
> 0.45 1.6762
> 0.55 0.5597
> 0.65 0.1154
> 0.75 0.0253
> 0.85 0.0020
> 0.90 0.0002
> 0.92 0.0001
> 0.94 0.0000
> 0.96 0.0000
> 0.98 0.0000
>
> Here is the input file for the calculation.
>
> Transformation of ILE 2 VAL Equilibration:
>
> &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=0.96, klambda=6,
> cut=9.0,
> &end
>
> Transformation of ILE 2 VAL production phase
> &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=0.96, klambda=6,
> cut=9.0,
> &end
>
> So can anybody please point out the mistake and suggest to overcome it. Thanks
> for your suggestions.
>
> Regards
> Biswa Ranjan Meher
>
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