Thanks
That make sense.
/ Samuel
2010/2/19 Hannes Kopitz <Hannes.Kopitz.gmx.de>:
> Dear Samuel,
>
> Since I implemented the TI decomp I can answer your question regarding this part:
> The difference you obtain is actually no error.
> The reason for the difference is just that the average given in the CHECK DECOMP section is the average over the dVdl-values that have been written out every NTPR steps which is also true for the different components of dVdl, whereas the dVdl value and its components written in the DV/DL, AVERAGES OVER <NSTLIM> STEPS steps is as its title says the average over the values of all NSTLIM steps.
>
> Cheers!
> Hannes
>
>
> -------- Original-Nachricht --------
>> Datum: Fri, 19 Feb 2010 10:10:45 +0100
>> Von: Samuel Genheden <samuel.genheden.gmail.com>
>> An: AMBER Mailing List <amber.ambermd.org>
>> Betreff: [AMBER] TI calculation of absolute dG with restraint and energy decomposition
>
>> Hello
>>
>> I've previously posted questions about my efforts to calculate
>> absolute dG of benzene to T4-lysozyme using TI in Amber 10. I will
>> follow the work by Roux, as cited in the Amber manual (JCTC 2 p1255).
>> This means that I want to add a restraint to my benzene molecule, but
>> I would also like to do an energy decomposition. The restraint energy
>> should not be included in the dv/dl energies so I set dvdl_norest to
>> 1. Now I have run a few lambdas on the van der Waals-part, i.e.
>> perturbing an uncharged benzene to nothing but I'm confused about the
>> output of sander. Here is a part of the output for one of the lambdas
>>
>> DV/DL, AVERAGES OVER 100000 STEPS
>>
>>
>> NSTEP = 100000 TIME(PS) = 320.000 TEMP(K) = -0.17 PRESS =
>> 0.0
>> Etot = -8.9561 EKtot = -8.9561 EPtot =
>> -22.2126
>> BOND = 0.0000 ANGLE = 0.0000 DIHED =
>> 0.0000
>> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
>> 8.8226
>> EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
>> -31.0353
>> EAMBER (non-restraint) = 8.8226
>> DV/DL = -53.2479
>> Ewald error estimate: 0.3153E-14
>>
>> ------------------------------------------------------------------------------
>> CHECK DECOMP - TOTAL ENERGIES (w/ REST)
>>
>> INTERNAL= 0.0000
>> VDWAALS = 8.8135 EEL = 0.000
>>
>> In a usual TI run, without restraint the EPTot is equal to DVDL, as
>> EPTot = V1-V0. But EPtot is also, in this case, VDWAALS+RESTRAINT as
>> it should be. But then I see that DV/DL, in this case is
>> EPtot+RESTRAINT=VDWAALS+2*RESTRAINT, although I do NOT want to include
>> the restraint energy in the dv/dl energy. In my book, if the only
>> thing I'm perturbing is the van der Waals-energy, the dv/dl energy
>> should be equal to the van der Waals-energy, i.e. ~8 kcal in this
>> case. Am I wrong?
>>
>> And then about the decomposition, if I understand it correctly, the
>> total VDWAALS part in the decomposition should add up to the VDWAALS
>> energy in the DV/DL summary. But here I see a small difference on the
>> second decimal. Is this just an numerical issue, or I'm wrong in my
>> interpretation?
>>
>> Best regards,
>> Samuel
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Feb 20 2010 - 03:30:02 PST
