Hi Samuel,
are you using soft core potentials? There are additional non-linear
contributions to dvdl that are not given in the normal amber energy
output, but in the soft core section below that.
Kind Regards,
Thomas
On Wed, February 24, 2010 4:03 am, Samuel Genheden wrote:
> Hello
>
> I posted this question along with another one last week, but since I
> only got answers on one of my questions I'm reposting this question in
> hope that somebody could help me.
>
> I want to calculate the 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. 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
>
> 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 with my assumptions? Could anybody clear things out
> for me?
>
> Best regards,
> Samuel
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 24 2010 - 04:00:02 PST
