Yet another NAMD speed concerns

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Sat Apr 25 2009 - 04:44:44 CDT

Hello,

I am running a simulation of my protein in water (cell = 15 angstroms
from the protein). System contains 110349 atoms total.
I have compiled namd 2.6 on xeon infiniband cluster uusing amd64
installation procedure. I`ve also used icc and ifort with -xSSSE3
flag.

My force field parameters are
=====================
exclude scaled1-4
1-4scaling 1.0
cutoff 15.
switching on
switchdist 10.

My integrator parameters are
=====================
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 4
stepspercycle 20

I use
====
langevin on
langevinPiston on

cellBasisVector1 108 0. 0.
cellBasisVector2 0. 102 0.
cellBasisVector3 0. 0 105.
cellOrigin 63.87940979 13.3578186035 32.2524185181

PME yes
PMEGridSizeX 125
PMEGridSizeY 125
PMEGridSizeZ 125

MY PROBLEM IS THAT MY SYSTEM IS TOO SLOW
======================================================
Utilization of 256 x Xeon 3Gz CPUs requires 41 hours for 10 ns
!!!!!!!!!!!!!!!!!!!
======================================================

I consider my system to be of a typical size. 100k atoms fro 10 ns is
normal in our days. But it is very hard calculate with NAMD even on
modern clusters.

1/ Is this speed normal for namd or did i do something wrong?
2/ Can I use 4fs for timestep with this parameters?
3/ what do you do to shortcut your calculations?

Thanks
SDA

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