Subject: Molecular dynamics with implicit solvent

From: Ibrahim Moustafa <[email-masked]>
Date: Sat, 15 Dec 2001 22:29:32 +0000 (GMT)

Dear ccl users,

   I'm doing MD on my protein structure without explicit solvents because
of the limiting computing power. I use Tripos FF, in SYBYL6.6; cutoff
distance 15 A, distance dependent dielectric function with dielectric
constant 2.

   First, I heat the system to 300 K in steps ( 10, 50, 100, 200, 300 K),
2 ps for each step.
   
  Comparing the resultant configuration of the heating step with the
starting configuration gives ( rmsd 3.79 A ). Of course the absence of
solvents is responsible for this nonsense movements. Now I'm thinking to
do the simulation at low temperature ( 50 K ) to supress these large
movements. I want to discuss this with ccl users before doing so.

  What I want to ask about is: suppose i conduct this simulation at 50 K
instead of 300 k, non physiological condition, ( I have seen some people
doing that " Journal of molecular structure (theochem) 368;1996: 205-212")
Can we rely on the output results of that kind of simulation? can we realy
trust the answer for the question under investigation?

  -Another question: in absence of solvents do we need to equilebrate the
system before the production phase in the MD? if so, WHY?

  - Is it better to start the simulation from the average structure of the
heating step ( or the equilebration step ) or start from the last
configuration of each step??

   I'd be really appreciated if someone answered these questions. I
promise I'll sumarize the answer to the CCL users.

  Many thanks,
   Ibrahim

Name         :Ibrahim M.Moustafa
Mail address :Center for Biomolecular Science,
              BIOMOLECULAR SCIENCE BUILDING,
              North Haugh,St-Andrews,
              Fife,KY16 9ST
              Scotland,U.K.
         Tel :+44(0)1334-467257
      E-mail :[email-masked]