Re: AMBER: problem regarding implicit simulation

From: Carlos Simmerling <>
Date: Mon, 23 Apr 2007 07:30:34 -0400

probably because you don't use a cutoff of 300 for explicit water simulation.
large proteins in implicit water are usually slower to simulate than
in explicit
water, there are more nonbonded pairs to calculate. explicit water usually
is done with periodic boundary conditions which can use methods like PME
to make the simulation faster..

On 4/23/07, gurpreet singh <> wrote:
> 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 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
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Received on Wed Apr 25 2007 - 06:07:18 PDT
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