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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 22 2017 - 16:00:02 PDT
