Dear Amber user,
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.
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
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- application/octet-stream attachment: min.in
- application/octet-stream attachment: eq2.in
- application/octet-stream attachment: eq1.in
Received on Wed May 19 2010 - 09:00:03 PDT
