Hi,
DVDL calculates the lambda-derivative of the total energy. This simplifies
to the difference between V0 and V1 plus a few correction terms for the
soft core potentials (see the 2007 J Chem Phys paper for the equations
etc.). You can not obtain DVDL from the softcore energy terms reported in
the output.
Kind Regards,
Thomas
On Tue, August 13, 2013 12:26 am, psu4.uic.edu wrote:
> Dear Amber,
>
> After reading the Amber manual and a couple TI related publication, I
> have a quite navy question: How can Amber calculate DV/DL during TI
> calculation?
>
> It looks to me that it is the summation of some energy terms of the
> softcore part of the system, but not very sure which terms are included
> and
> which are not.
>
>
> Here is an example:
>
> NSTEP = 250 TIME(PS) = 100.250 TEMP(K) =
> 301.06 PRESS = 223.5
> Etot = -90941.2828 EKtot = 38415.3548 EPtot =
> -129356.6376
> BOND = 25991.2281 ANGLE = 2055.7814 DIHED =
> 4213.1786
> 1-4 NB = 930.7284 1-4 EEL = 12548.9046 VDWAALS =
> 24113.5279
> EELEC = -199209.9866 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> *DV/DL = 10.6266*
> EKCMT = 11611.7978 VIRIAL = 9618.8596 VOLUME =
> 412937.7546
> Density =
> 1.0526
> Ewald error estimate: 0.3218E-04
> ------------------------------------------------------------------------------
>
> *Softcore part of the system: 1 atoms, TEMP(K) =
> 1534.78*
> SC_Etot= 6.5438 SC_EKtot= 4.5748 SC_EPtot =
> 1.9689
> SC_BOND= 1.5838 SC_ANGLE= 0.3042 SC_DIHED =
> 0.0536
> SC_14NB= 0.0273 SC_14EEL= 0.0000 SC_VDW =
> 0.0000
> SC_EEL = 0.0000
>
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS=
> 0.0000
> SC_RES_PLPT= 0.0000 SC_RES_PLPL= 0.0000 SC_RES_GEN =
> 0.0000
> SC_EEL_DER= 0.0000 SC_VDW_DER= 2.9867 SC_DERIV =
> 2.9867
> ------------------------------------------------------------------------------
>
> Here are the energy terms of the other pair
>
> NSTEP = 250 TIME(PS) = 100.250 TEMP(K) = 301.03 PRESS =
> 223.5
> Etot = -90944.4775 EKtot = 38412.1601 EPtot =
> -129356.6376
> BOND = 25991.2281 ANGLE = 2055.7814 DIHED =
> 4213.1786
> 1-4 NB = 930.7284 1-4 EEL = 12548.9046 VDWAALS =
> 24113.5279
> EELEC = -199209.9866 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> * DV/DL = 10.6266*
> EKCMT = 11611.7978 VIRIAL = 9618.8596 VOLUME =
> 412937.7546
> Density =
> 1.0527
> Ewald error estimate: 0.3218E-04
> ------------------------------------------------------------------------------
>
> * Softcore part of the system: 1 atoms, TEMP(K) =
> 464.06*
> SC_Etot= 2.3169 SC_EKtot= 1.3833 SC_EPtot =
> 0.9336
> SC_BOND= 0.1251 SC_ANGLE= 0.3212 SC_DIHED =
> 0.0536
> SC_14NB= 0.4337 SC_14EEL= 0.0000 SC_VDW =
> 0.0000
> SC_EEL = 0.0000
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS=
> 0.0000
> SC_RES_PLPT= 0.0000 SC_RES_PLPL= 0.0000 SC_RES_GEN =
> 0.0000
> SC_EEL_DER= 0.0000 SC_VDW_DER= 2.9867 SC_DERIV =
> 2.9867
> ------------------------------------------------------------------------------
>
>
>
> The other question is that why DV/DL could fluctuate so wildly during
> the
> simulation? In one of the TI tutorials, the instantaneous
> DV/DL<http://ambermd.org/tutorials/advanced/tutorial6/images/xmgrace3_large.jpg>fluctuate
> significantly. I guess we can answer this question only after
> knowing which terms are included in DV/DL. Please forgive any ignorance,
> if any.
>
> Cheers,
> Henry
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Aug 13 2013 - 02:00:02 PDT
