AMBER Archive (2004)

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

From: Daniel Wetzler (danielwetzler_at_appleinfo.de)
Date: Sat Oct 23 2004 - 13:16:12 CDT

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.

>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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