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

From: Huang (huangloligo_at_gmail.com)
Date: Fri Aug 29 2008 - 08:33:57 CDT

Hi All,

In order to close the thread, I make this post.

I am sorry to disturb you before, but all the strange thing there was
because of misuse of NAMD. I find that if pressureProfile turned on,
any minimize will make NAMD get info sleep after output PPROFILEBONDED
and PPROFILENONBONDED at timestep 0. And neither PRESSUREPROFILE nor
PPROFILEINTERNAL are there.

I don't know if it is a bug (for no warning from NAMD and its ug, but
I did not check the src code). But I think seldom people will use
NAMD in the manner what I did a few days ago. It is obvious that when
minimizing, there is no pressure at all.

Thank you for your attention!

2008/8/28, Huang <huangloligo_at_gmail.com>:
> 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
> ============================
>

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

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