Hi, Thomas
Yes, I am using soft cores. The other part of the average part of the
output is like this
A V E R A G E S O V E R 100000 S T E P S
NSTEP = 100000 TIME(PS) = 320.000 TEMP(K) = 299.97 PRESS = 0.5
Etot = -76072.0962 EKtot = 15847.2682 EPtot = -91919.3645
BOND = 501.9319 ANGLE = 1261.8232 DIHED = 1762.2574
1-4 NB = 603.4801 1-4 EEL = 5271.4225 VDWAALS = 14135.2790
EELEC = -115457.1104 EHBOND = 0.0000 RESTRAINT = 1.5518
EAMBER (non-restraint) = -91920.9162
DV/DL = -53.2479
EKCMT = 6974.8427 VIRIAL = 6972.1773 VOLUME = 255849.8846
Density = 1.0286
Ewald error estimate: 0.1259E-03
------------------------------------------------------------------------------
Softcore part of the system: 12 atoms, TEMP(K) = 299.87
SC_BOND= 2.0344 SC_ANGLE= 2.8304 SC_DIHED = 2.7101
SC_14NB= 3.8823 SC_14EEL= 0.0000 SC_EKIN = 8.9384
SC_VDW = -0.1673 SC_DERIV= -1.3284
------------------------------------------------------------------------------
NMR restraints: Bond = 3.513 Angle = 21.118 Torsion = 9.949
I though that the energies written under the DV/DL, AVERAGES section
(the output I posted previously) contained all energies that were
included in the DV/DL. So if I have soft-core turned on,
DV/DL=V1-V0+SC_DERIV, or? Even if so, the SC_DERIV energy is on
average -1.3284 and the numbers still not add up. DVDL is not equal to
VDWAALS - RESTRAINTS + (SC_DERIV) or am I getting this all wrong. Am I
completely off assuming that all contributions to the DV/DL should
come from the van der Waals part (including SC_DERIV) if I'm only
perturbing that part of the system.
/ Samuel
2010/2/24 <steinbrt.rci.rutgers.edu>:
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 24 2010 - 04:30:03 PST
