AMBER Archive (2004)

Subject: Re: AMBER: MD problem (very long parhabs endless runtime)

From: myang_at_vitamin.uni.cc
Date: Sat Oct 23 2004 - 13:35:59 CDT

On Sat, Oct 23, 2004 at 08:16:12PM +0200, Daniel Wetzler wrote:
> Hi Ross,
>
> thanks for your answer !
> Unfortunately I couldn't solve the problem yet.
>
> >Do you get any output at all? E.g. if you look in the mdout file has the
> >input file at least been reported here?
> >
> >
> >
> No I didn't get any output.
Since you got no output, I believe it's problem of your machine
environment. How do you run the sander program?

>
> >Also, how big is your system? A single step for anything up to 100,000
> >atoms
> >really should not take more than a minute at most.
> >
> >
> My system is much smaller. It owns only about 10000 atoms including
> about 2000 Water molecules.
>
> >Are you running this on a single cpu? Or in parallel on the machine?
> >(mpirun). Also do the test cases all pass? It likely that if you are
> >getting
> >no output at all that you sander installation is corrupt. If the test cases
> >all pass then this is much more unlikely.
> >
> >
> Uh. I didn't check that. Where do I find these test cases ?
>
>
> >>molecular dynamics
> >>&cntrl
> >> irest = 0, ntx = 1,
> >>
> >>
> >
> >This bit looks fine.
> >
> >
> >
> >> ntb = 2, ntp = 0,
> >>
> >>
> >
> >This part of your input is inconsistent. You are requesting a constant
> >pressure run (ntb=2) but then set there to be "NO" pressure scaling
> >(ntp=0).
> >This is likely to be the cause of your problem if all the test cases pass.
> >However, sander should really have produced an error message in this
> >situation.
> >
> >
> I changed the settings to 1 but didn't get any output yet.
>
>
> >> nstlim = 10,
> >>
> >>
> >
> >If you really only want one step you should set this to nstlim=1. Note btw,
> >if you are interested in just obtaining the energy for the "current"
> >structure then you are better off doing a single step of minimisation
> >rather
> >than MD. (set imin=1 and maxcyc=1). In this way the energy of the initial
> >structure will be calculated but no actual structural changes will take
> >place.
> >
> >
> >
> I wanted to set it to one just to check wheteher MD works onmy system.
> If it runs I want to
> perform a run of much more steps.
>
> >> dt = 0.001,
> >> ntpr = 1,
> >> ntwx = 1,
> >>
> >>
> >
> >This is fine.
> >
> >
> >
> >> ntwv = 1,
> >>
> >>
> >
> >Do you 'really' want to write out the velocities every step? If at all?
> >
> >
> >
> Only for my test run later I would set this value to 100.
> <>
>
> Belly should work but is not recommended practice any more. Especially if
> you are trying to do constant pressure MD. This is unlikely to give you a
> stable simulation. I would avoid belly for anything other than
> minimisation...!!! And even then you are probably better using restraints
> instead.
>
>
> Oh, that's a good hint. But why is belly so bad ?
>
> >
> >I hope this all helps...
> >All the best
> >Ross
> >
> >
> Thanks a lot. I think I will search for examples to test my sander
> installation.
>
> Best wishes,
>
> Daniel
>
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