AMBER Archive (2007)

Subject: AMBER: regarding implicit simulation

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Tue Aug 14 2007 - 01:21:35 CDT

Hello Users
 i have a general question on implicit simulation method. I will ask with
an example, say a protein needs one water molecule to be present at a
particular point for it to behave normally during the simulation.
Now in implicit simulation since we are not having any water as such but we
are using the dielectric constant similar to water, my question is, will the
simulation in such solvent will give us the same structural changes as we
were expecting .

Although i know that in general that much difference in the movement will be
there if we compare explicit and implicit but i want the answer with respect
to the above example.

I hope my question is clear.

Thanks & Regards
Gurpreet
IIT MADRAS
INDIA

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