Molecular dynamics with implicit solvent

[Ibrahim Moustafa <im17 ^at^ st-andrews.ac.uk>]

 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 :im17 ^at^ st-andrews.ac.uk