AMBER Archive (2003)

Subject: Re: GB vs. explicit solvent calculations

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Thu Mar 20 2003 - 08:25:12 CST

one possibility is that there is no pairlist in
the GB calculation, so all pairs are considered
at each step, the cutoff saves some (but not all)
of the effort for pairs farther apart than cutoff.
The explicit solvent code is more efficient in that
respect.

Other things may be involved as well.
You can compare the breakdown of timings for
each part of the calculation given at the end of the run.
Carlos Simmerling

----- Original Message -----
From: "Thomas Steinbrecher" <thomas.steinbrecher_at_physchem.uni-freiburg.de>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Thursday, March 20, 2003 8:53 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
> expected?
> 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
> &cntrl
> imin=0,
> ntc=2, ntf=2,
> cut=24.0, igb=1, saltcon=0.2, gbsa=0,
> ntpr=50,
> nstlim = 5000, dt=0.002,
> ntt=1, tempi=0.0, temp0=300.0, tautp=1.0,
> ntx=1, irest=0, ntb=0,
> nscm = 1000,
> ntr=1,
> &end
> keep all atoms frozen
> 1.0
> RES 1 255
> END
> END
>
>