RE: GB vs. explicit solvent calculations

From: Yong Duan <>
Date: Thu, 20 Mar 2003 09:48:30 -0500

This is because your cutoff 24 A in GB is twice the cutoff you used in
explicit water simulation. This increases the number of pairwise
calculations substantially, despite the fact that your system in GB is


-----Original Message-----
From: Thomas Steinbrecher
Sent: Thursday, March 20, 2003 8:54 AM
Subject: GB vs. explicit solvent calculations

Dear AMBER users,

I am conducting MD simulations on a 200 aar protein
complexed with a ligand using AMBER7 on a Beowulf linux cluster.

I recently tried to perform a generalized Born simulation following the
guidelines in the GB tutorial on the AMBER homepage instead of my
previous approach with appr. 6000 molecules of TIP3P solvent.

I am using the standard pairwise GB model with IGB=1 and saltcon=0.2
with a 24A cutoff. My ligand is parametrized with the gaff-forcefield
and I have applied bugfix 24

>From my output files I see that 1ps of equilibration takes
1300 sec. with explicit solvent (cutoff 12A), while it
takes 2700 sec. using the GB model, both calculated on a
dual processor PC.

I rather expected the GB calculation to be faster, even
with the inclusion of salt effects.
Did I do something wrong or is this behaviour to be
Can it be due to the size of my system or due to the
varying cutoff?
Is it possibly related to the fact that I run parallelized sander?

I was wondering if anyone can share experiences regarding
the performance of the different GB models in terms of
speedup compared to explicit solvent simulations.

Many thanks in advance,

Thomas Steinbrecher

My sander input file is:
  equilibrate structure
   ntc=2, ntf=2,
   cut=24.0, igb=1, saltcon=0.2, gbsa=0,
   nstlim = 5000, dt=0.002,
   ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
   ntx=1, irest=0, ntb=0,
   nscm = 1000,
  keep all atoms frozen
RES 1 255
Received on Thu Mar 20 2003 - 14:53:02 PST
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