I am writing the message while somehow sent it out before I finished it...
This email is the one with complete information.
Sorry for the duplicated messages. --Yan
Dear Amber users,
I am simulating a molecule in both explicit and implicit model to help
myself understand these two models.
The molecule contains 3200 atoms, and the water molecules for the explicit
simulation is ~50000.
Below are two example inputs and outputs:
------------------------------
--------------explicit-----------------------------------------------------------------------------
*inputs:*
imin = 0,
ntb=2,ntc=2,ntf=2,ntp=1,
taup=2.0,
igb = 0, ntpr = 100, ntwx = 1000,ntwe=100
ntt = 3, gamma_ln = 5.0,
temp0 = 300.0
nstlim = 100000, dt = 0.001,
cut = 10.0
*outputs:*
NSTEP = 12000 TIME(PS) = 12.000 TEMP(K) = 301.74 PRESS =
-347.7
Etot = -122182.2229 EKtot = 32579.1028 EPtot =
-154761.3257
BOND = 1292.3443 ANGLE = 2238.1662 DIHED =
5343.3138
1-4 NB = 2610.8184 1-4 EEL = 2556.6335 VDWAALS =
21371.0486
EELEC = -190173.6505 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 15089.3793 VIRIAL = 19350.8098 VOLUME =
567683.6783
Density =
0.9640
Ewald error estimate: 0.2249E-04
----------------------------------------------------------------------------------------------------------------------------------
--------------------------------------------implicit------------------------------------------------------------------------------
*inputs*:
imin = 0, ntb = 0,
igb = 1, ntpr = 100, ntwx = 1000,ntwe=100
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0,
nstlim = 100000, dt = 0.001,
cut = 10.0,
*outputs:*
NSTEP = 10000 TIME(PS) = 10.000 TEMP(K) = 297.03 PRESS =
0.0
Etot = 6201.4280 EKtot = 2939.5018 EPtot =
3261.9262
BOND = 1723.6155 ANGLE = 2172.3379 DIHED =
5109.8466
1-4 NB = 2533.9085 1-4 EEL = 2697.4634 VDWAALS =
-1182.1961
EELEC = -836.8758 EGB = -8956.1738 RESTRAINT =
0.0000
----------------------------------------------------------------------------------------------------------------------------------
I have few questions:
1. What do EKCMT and VIRIAL stand for in explicit simulation output?
2. I understand that the potentials will change due to different total atom
number, but when I sum BOND, ANGLE, AND HIHED, I got similar energies for
implicit and explicit simulations, say, both around 14000 kcal/mol. For the
implicit simulation, the summation energy should be that for the molecule.
While for the explicit simulation, should that summation energy also include
those from water? or water molecules do not contribute to these energies?
3. The total energy is positive for implicit simulation, and negative for
the explicit simulation. In the implicit one, the bond/angle/dehi energies
are dominant, while in the explicit one, the electro-static energy from
water molecules are more dominating. Am I understanding it correctly? Is the
bond/angle/dehi energies looks normal? Is the positive total energy normal?
4. I am trying to study the binding energy of a several-molecule-complex. If
the positive total energy (for individual molecule) is acceptable, I suppose
that I should focus on the difference of the solvation energies (or, ~ the
total energy) of the complex and individual molecules. Am I right?
Any input is appreciated!
Regards,
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Tue Aug 10 2010 - 16:00:05 PDT
