Hi Dave,
I see now. Thanks for your reply! I’m just doing TI here actually.
Hope you’re doing well!
Lin
> On Aug 22, 2017, at 7:01 PM, David Cerutti <dscerutti.gmail.com> wrote:
>
> 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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>>
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Received on Tue Aug 22 2017 - 17:00:02 PDT
