Re: Coarse-Graining MD don't work perfect as expected

From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Fri Dec 30 2011 - 03:57:44 CST

Hi Zhonghe,

do you have any error messages.

Thanks,

Boyang

2011/12/29 ΠμΦΣΊΣ <zhhxu_at_mail.ipe.ac.cn>

> Hi all
> I have run a coarse-grain simulation on a computer with 8 cores(intel(R),
> E5620,2.4GHz)+4 GPUs(tesla C2050),
> it seem weird to me that it took twice times as all-atom-simulation(enen
> the num of atoms is almost 1.5 times as CG-beads).
> The conf file is listed below. I want to know where I have gone wrong.
> Thanks in advance for your suggestion.
> with best wishs for you
> zhh.xu
> graduate student
> Institute of Porcess Engineering , Chinese Academy of Science
> #################################################################
> # 61540 atoms 18359 bonds 186420 degree of
> freedom #
> # Wallclock 1116189 cputime 1115864 Benchmark time
> 0.2364 s/step #
> ##################################################################
> parameters input/rbcg-2007.par
> exclude 1-2
> cutoff 12.0
> switching on
> switchdist 9.0
> pairlistdist 16.0
> dielectric 20.0
> hgroupcutoff 0
> margin 4
> # Integrator Parameters
> timestep 20.0
> nonbondedFreq 1
> stepspercycle 10
> wrapAll on
> #PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 250
> PMEGridSizeY 250
> PMEGridSizeZ 135
> # Constant Temperature Control
> langevin on
> langevinDamping 5.0
> langevinTemp 300
> langevinHydrogen off
> # Constant Pressure Control (variable volume)
> useGroupPressure yes
> useFlexibleCell yes
> useConstantArea no
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200.
> langevinPistonDecay 50.
> langevinPistonTemp 300
> # Minimization
> minimize 2000
> reinitvels 300
> run 500000 ;# 10ns
> ###########
>
>
>
>
>
>
>

-- 
Boyang Wang, Ph.D.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:38 CST