> I am trying to do dynamics to estimate solvation of sugar molecule in water
> and ionic liquid.
> I have some problem with Etot value.
> The Etot value about solvation in water after equilibration is negative. But
> this value about ionic liquid is positive.
The bulk of the positive energy in your ionic liquid is:
> 1-4 EEL = 20428.0423
This may be ok, but insofar as you're worried about the energy,
your charge derivation scheme is what you should look at.
> Gaussian03-RESP and GAFF.
What basis set? I am not an expert here, but it seems like charged
molecules might be especially sensitive to the quantum method used.
Also I see:
> Density = 1.4534
Is this empirically correct? This is probably more critical than
the energy being positive. The energy in molecular mechanics is
somewhat arbitrary, and in general one can compare energies
only between different conformations of the same system.
Bill
> Does it means that all of the molecule in the ionic liquid simulation box is
> unstable? If yes, how can I get more stable value.
> Attached files are the min.in and eq1.in eq2.in that were used for
> minimization and equilibration process.
> Ionic liquid is not standard solvent in AMBER, so I made it by using
> Gaussian03-RESP and GAFF. And then 2-equilibration step were used before
> production run.
> WATER + GLUCOSE (minimization step + constant volume(gradually heating up at
> 300K for 200ps) + constant pressure(1bar for 500ps)
> ----------------------------------------------------------------------------
> -----------------------------
> NSTEP = 500000 TIME(PS) = 700.000 TEMP(K) = 301.50 PRESS =
> 234.3
> Etot = -39970.1873 EKtot = 10087.8912 EPtot =
> -50058.0786
> BOND = 113.9221 ANGLE = 298.9855 DIHED =
> 412.4544
> 1-4 NB = 106.7991 1-4 EEL = 1354.4259 VDWAALS =
> 7347.7947
> EELEC = -59692.4603 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 4841.9279 VIRIAL = 3994.8560 VOLUME =
> 167457.0753
> Density =
> 1.0028
> Ewald error estimate: 0.1920E-01
> ----------------------------------------------------------------------------
> ------------------------------
> Ionic liquid(1-ehtyl-3-methylimidazolium Trifluoromethylsulfonate) + Glucose
> (First, Making a solvent box then, 2-step equilibration(same as above) ->
> put the glucose molecule -> minimization -> 2-step equilibration(same as
> above)
> ----------------------------------------------------------------------------
> ------------------------------
> NSTEP = 500000 TIME(PS) = 700.000 TEMP(K) = 296.54 PRESS =
> -41.5
> Etot = 23333.2118 EKtot = 5628.0211 EPtot =
> 17705.1907
> BOND = 8808.3268 ANGLE = 6609.1757 DIHED =
> 1606.4478
> 1-4 NB = 309.9771 1-4 EEL = 20428.0423 VDWAALS =
> -2890.1536
> EELEC = -17166.6255 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 476.8408 VIRIAL = 551.2372 VOLUME =
> 82969.3878
> Density =
> 1.4534
> Ewald error estimate: 0.9427E-04
> ----------------------------------------------------------------------------
> ------------------------------
> Thanks in advance.
> Regards,
> Hoshin Kim
> ----------------------------------------------------------------------------
> -------
> Hoshin Kim
> Now)
> Visiting Scholar
> Department of Chemical and Biomolecular Engineering
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-986-9258
> Also)
> Graduate student (M.D. candidate)
> Ionic Liquids Team(ILs) in Bio Nano Process Lab
> Department of Biological Engineering,
> 2S 113, Engineering building Inha University,
> 253 Yonghyeon Dong, Nam Ku
> Incheon, KOREA
> TEL) +82-32-860-8655
> ----------------------------------------------------------------------------
> -------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 19 2010 - 10:30:04 PDT
