Hi, all:
I am writing to you to get some suggestions about energy terms of amber MD.
My system is one 1,2-dichloroethane molecules and 62 cyclohexane molecules.
Firstly, the charges and mol2 files of 1,2-dichloroethane and cyclohexane are obtained by
using antechamber and generalized amber force field according to tutorial B4, i.e,
antechamber -i cyclohexane.pdb -fi pdb -o cyclohexane.mol2 -fo mol2 -c bcc -s 2
The prmtop and inpcrd files are generated by tleap.
Then, the minimization and equilibration are performed for the whole system.
After equilibration, the energy terms for one snapshot of MD simulations are shown in the following:
NSTEP =300 TIME(PS) = 2022.300 TEMP(K) = 298.81 PRESS = 404.4
Etot = 1744.8560 EKtot=1001.1405 EPtot = 743.7155
BOND = 360.1777 ANGLE = 475.9516 DIHED = 208.4958
1-4 NB = 187.9432 1-4 EEL = -52.7059 VDWAALS = -525.4131
EELEC = 89.2662 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 61.6986 VIRIAL = -39.6589 VOLUME = 11608.5115
Density = 0.7605
Ewald error estimate: 0.4121E-03
Please note that Etot = 1744.8560 and EELEC = 89.2662, they are both positive values, is there something wrong?
I have checked the energy terms in the amber tutorial and found that both the EELEC values and Etot values are very negative.
Any suggestions will be helpful.
Best wishes,
Yuan Dandan
Nanjing University, China
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Received on Wed Apr 20 2016 - 07:00:03 PDT
