# Re: [AMBER] Thermodynamic Integration question

From: David Cerutti <dscerutti.gmail.com>
Date: Tue, 22 Aug 2017 19:01:29 -0400

If the TI is happening irrespective of the restraint, then you just use the
EAMBER (non-restraint) energy, which in this case is identically EELEC. I
think this is what you'd want in your case, although it looks like you may
be trying to do TI on top of WHAM, and I don't know if there could be
unexpected problems there (I don't know that it is wrong, I just haven't
seen it before).

On Tue, Aug 22, 2017 at 6:51 PM, Lin Song <qxsxmu2010.gmail.com> wrote:

> Dear AMBER user:
>
> I’m running PMEMD TI calculations and meet a question. I’m disappearing
> the charge of an ion and the two end states are:
>
> V0: Protein—ion, with ion restraint in the protein;
>
> V1: Protein—neutral atom, with same positional restraint as V0.
>
> The output gives me DV/DL, but that DV/DL includes contribution from
> positional restraint. To exclude the contribution from positional
> restraint, do I just use the EELEC term? As you can see, below the output.
>
> ------------------------------------------------------------
> ------------------
>
>
> DV/DL, AVERAGES OVER 1000 STEPS
>
>
> NSTEP = 5000 TIME(PS) = 735.000 TEMP(K) = 3.00 PRESS =
> 0.0
> Etot = 0.0000 EKtot = 0.0000 EPtot =
> 73.1496
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> 0.0000
> EELEC = 77.0602 EHBOND = 0.0000 RESTRAINT =
> -3.9106
> EAMBER (non-restraint) = 77.0602
> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
> 0.0000
> Density =
> 0.0000
> DV/DL = 73.1496
> Ewald error estimate: 0.0000E+00
> ———————————————————————————————————————
>
> Best,
> Lin
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Received on Tue Aug 22 2017 - 16:30:02 PDT
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