Hello,
On Tue, Aug 10, 2010 at 6:32 PM, Yan Gao <yan.gao.2001.gmail.com> wrote:
> 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?
>
I think these are PME terms, but I don't know much about PME so someone else
will have to comment here (or see the relevant literature).
> 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?
>
Obviously, there is no dihedral term in water molecules. However, you used
ntc=2, ntf=2 in the explicit solvent calculation, so any bonded potential
terms involving hydrogen aren't calculated (because ntf=2), and in any case
they are restrained to their equilibrium values (because ntc=2), so the
water molecules won't add to those terms. Another couple comments: you
should probably be using a much larger value for CUT in your implicit
solvent calculation since electrostatic interactions are still significant
past 10 Angstroms (in explicit solvent, only VDW is cut off at cut since EEL
is still accounted for by PME). Why are you using SHAKE in explicit but not
in implicit?
Good luck!
Jason
>
> I am trying to study the binding energy of several molecules.
>
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 10 2010 - 16:00:07 PDT
