AMBER Archive (2009)

Subject: [AMBER] Density in MD simulation

From: Ibrahim Moustafa (I.moustafa_at_psu.edu)
Date: Fri Apr 17 2009 - 11:09:16 CDT

Dear Amber users,

  Iım trying to do MD for a protein solvated (TIP3PBOX) in a truncated
Octahedron cell (12 A distance from protein atoms to the edge) using Amber10
and ff99SB.
Currently, Iım at the equilibration stage. I noticed that the density is a
bit higher than it should be (1.0430, a little bit off from 1.0000). The
following input parameters are used:

-----------------input file-----------------------
 &cntrl
   imin=0, irest=1, ntx=5,
   ntpr=1000, ntwx=1000, ntwr=1000,
   cut = 9.0, nsnb = 10, scnb = 2.0, scee = 1.20,
   nstlim=350000, dt=0.001,
   ntt = 1, tautp=2.0, taup=0.2, temp0=300.00,tempi=300.00,
   ntb = 2, ntf = 2, ntc = 2, ntp = 1,
   nscm = 500,
 &end
 &ewald
    use_pme=1,
 &end
/
-----------------------------------------------------

I tried to use different distances (shorter and longer) when solvating the
system and the density behaves the same way, always reach the point where
fluctuating around 1.0400. I wonder if there is a way to bring the density
closer to 1.0000. In previous simulations for slightly different systems,
usually, I have the density fluctuating around 0.998 & 1.020.
Iım a little worried about the artifacts in the simulation because of the
density value. Actually, Iım not sure how bad the effect could be!
  Any comment, suggestions would be appreciated.

 Googling and looking through AMBER archive could not help to find an answer
to my question.

  thanks,
 Ibrahim

           
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber