[AMBER] Solvation in water

From: Hoshin Kim <85hskim.gmail.com>
Date: Fri, 2 Jul 2010 11:39:42 +0900

Dear amber user,

I'm trying to do sugar solvation simulation in water(liquid state). I want
to know that my result of simulation has been solvated in liquid water.
Because the distance between water molecules are too far to calculate h-bond
energy. It means water molecules were scattered like gas state.
I did equilibration in NVT/NPT at 300K. and density is correct(almost 1.00).
production run has been carried out for 4.5ns at 300K (NPT).
Attached herewith is result PDB file. Please check this file and tell me
whether that sugars are in liquid sate water. If it is not liquid state, how
can I do solvation simulation in liquid state water box?

Thank you in advance.

(8-glucose molecules are put into TIP3PBOX which was used as water box.)


Hoshin Kim,

Hoshin Kim
Visiting Scholar
Department of Chemical and Biomolecular Engineering
North Carolina State University
Raleigh, NC 27695
Phone: 919-986-9258
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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Received on Fri Jul 02 2010 - 09:00:03 PDT
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