Have you tried watching a movie of the trajectory in something like VMD?
E.g. watch it during the constant volume phase and then watch it during the
constant pressure phase. You might be able to see what happens. You could
also try, if things are not too big, recording the mdcrd file every 5 steps
or so (ntwx=5), then you will be able to clearly see what happens.
In the meantime try looking at some other data about your simulation.
Pressure, volume, energy, temperature etc. Things probably start to go wrong
long before the simulation is stopped. (did you minimise before starting
MD?, what temperature regulation are you using, what is your time step?...)
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Li Su
> Sent: Wednesday, August 24, 2005 10:36
> To: amber.scripps.edu
> Subject: AMBER: a problem encountered when trying to
> equalibrate alanine dipeptide in explicit water
>
> Dear Amber User,
>
> I encountered a problem when tried to equalibrate alanine
> dipeptide in
> explicit water. After equalibrating ala2 in water with a
> small restraint on
> ala2 with constant volume, I started to equalibrae it with constant
> pressure. But it always stopped after several steps of
> equalibration, show
> ing an error message at the bottom of the amber output file
> like following,
>
> vlimit exceeded for step 1390 ; vmax = 431.631598201490
>
> Coordinate resetting (SHAKE) was not accomplished
> within 3000 iterations
>
> I thought it might be the problem of not well enough
> equalibrated in the
> constant volume stage. So I tried to elong the time used for
> the stage from
> 20ps to 100 ps, but it seemed not to help. If you have any
> idea about this
> problem, could you please tell me. Thank you in advance.
>
>
>
> Bese Wishes,
> Li
>
>
>
> --------------------------------------------------------------
> ---------
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Received on Wed Aug 24 2005 - 18:53:00 PDT
