AMBER Archive (2007)

Subject: AMBER: problem regarding implicit simulation

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Mon Apr 23 2007 - 01:16:35 CDT

Hello Amber users

i m using Amber 9 to carry out implicit simulation of a protein molecule
containing around 3000 atoms but i found that the mini. or equi. in implicit
solvent is much slower than the mini or equi.in the explicit solvent , i
think for this much no of atoms the simulationshud be faster the explicit ,
please tell me the reason for this unusual behaviour

following are the input files i m using :
for mini.

 imin=1,igb=2,cut=300.0,maxcyc=500,ncyc=250,ntr=1,ntb=0

for equi.

 imin=0,igb=2,cut=300.0,ntr=1,ntb=0,nstlim=20000,dt=0.002,ntc=2,ntf=2,
   tempi=10.0,temp0=300.0,ntt=1,tautp=2.0,ntp=0,ntpr=100,ntwx=0

thanks

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu