Re: AMBER: thermodynamic integration

From: David A. Case <case.scripps.edu>
Date: Fri, 9 Nov 2007 10:27:48 -0800

On Fri, Nov 09, 2007, Cooper, Matthew wrote:

> For the jobs, which remove the charge on a solvated molecule to measure
> the free energy of charging, there are two types of input decks:
>
> For the first part:
>
> Imin = 0, irest = 0,
> Nstlim = 100000,
> Ntx = 1, ntb = 2, ntp = 1, ntt = 1,
> Tautp=1, tauup=5, temp0=298.0,
> Ntave=1250, dt=0.002,
> Ntc =2, ntf = 2, cut = 9.,
> Ntpr = 125, ntwe = 125, ntwx = 125, iwrap = 1,
> Scee = 1.2, icfe = 1,
> Clambda = 0.0,
>
> For the next 5 parts (where clambda equals 0.2, 0.4, 0.6, 0.8 and 1.0
> respectively and the two states are charged and uncharged)
>
> Imin = 0, irest = 1,
> Nstlim = 100000,
> Ntx = 5, ntb = 2, ntp = 1, ntt = 1,
> Tautp=1, tauup=5, temp0=298.0,
> Ntave=1250, dt=0.002,
> Ntc =2, ntf = 2, cut = 9.,
> Ntpr = 125, ntwe = 125, ntwx = 125, iwrap = 1,
> Scee = 1.2, icfe = 1,
> Clambda = 0.2,

These give the input files, but not the rest of the arguments. I think
we need to see your groupfile to know exactly what you are doing.

As far as I can see(?), the only difference above is in the value of clambda.
Why do you say that there are "two types of input decks"? You seem to be
saying that "the two states are charged and uncharged" in the second set but
not in the first? No matter what the value of clambda, you need to have two
prmtop files with different charges.

What we need is a *complete*, short (say nstlim=10, ntpr=1) example
that fails. This problem is unlikely to be solved unless someone can
reproduce it.

....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Nov 11 2007 - 06:07:46 PST
Custom Search