Re: Why turning on 'pressureProfile' make NAMD get into sleep?

From: Huang (huangloligo_at_gmail.com)
Date: Thu Aug 28 2008 - 08:20:15 CDT

Hi All,

I run this simulation on cluster managed by TORQUE and MAUI. I use
two computer each of which has 4 CPU. NAMD is
"NAMD_2.6_Linux-amd64-TCP.tar.gz".

Could anyone kindly show me a config file that can run and make NAMD
output pressure profile online? Or tell me how to find a tutorial
concerning the subject?

Please correct me if I missed something.

2008/8/25, loligo huang <huangloligo_at_gmail.com>:
> Hi All,
>
> I have tried to simulate a membrane system and calculated its lateral
> pressure profile, but every time the NAMD gets into sleep after output
> 'PRESSURE', 'GPRESSURE', 'PPROFILEBONDED' and 'PPROFILENONBONDED' at
> timestep 0. It is strange that neither 'PRESSUREPROFILE' nor
> 'PPROFILEINTERNAL' there.
>
> It is said in ug that "If the simulations are performed using PME, the
> Ewald contribution should be estimated using a separate, offline
> calculation based on the saved trajectory files," but I don't think it
> is my situation. I have turn off 'pressureProfileEwald' and want to
> calculate the pprofile online.
>
> Any help would be appreciated.
>
> My configuration file snippet:
> ====================================================
> set pressureProfile on
> .....
> timestep 2
> nonbondedFreq 2
> fullElectFrequency 4 #
> Change to 1 auto by namd when pprofile
> stepspercycle 20
>
> PME yes
> PMEGridSpacing 1.0
>
> useGroupPressure yes
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200
> langevinPistonDecay 100
> langevinPistonTemp $temperature
>
> useFlexibleCell yes
> useConstantRatio no
> useConstantArea yes
> surfaceTensionTarget 0
>
> if {[info exists pressureProfile]} {
> pressureProfile $pressureProfile
> pressureProfileSlabs 100
> pressureProfileFreq 500
> pressureProfileEwald off
> }
> ====================================================
>
> Thanks
>
>

-- 
Qingsheng Huang
============================
School of Life Sciences
Sun Yat-sen University, Guangzhou
============================

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