AMBER Archive (2008)

Subject: AMBER: using Velocity-Verlet algorithm

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Thu Jun 12 2008 - 07:07:20 CDT

        
        
        
        
        
        
        
        
        
        

Dear Amber users,

        
        
        
        
        
        
        
        
        
        

I'm trying to run Constant-pressure
constant-temperature MD simulations of DMSO ( Dimethyl Sulfoxide )-H2
O mixture at ambient conditions to evaluate structural and
dynamical properties.
 MD simulations will be carried out
 within
the NPT ensemble at T ) 303 K and p ) 1 atm
. I want to solve the
equations
 of motion using the Velocity-Verlet algorithm with
 the
time step of 1fs.
 Could you give me some urgent suggestions and
tips for using Velocity-Verlet algorithm ? And I'm using Amber 10 v. and I would like to use OPLS/AA force field for the simulations of biomolecular  systems  .  But I'm not sure if OPLS parameters are available and  OPLS or OPLS/AA are used in Amber 10 v. .
So ,
 Could you give me some information about this issue ?
        
        

Sincerely,

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