I set cutoff to 10 for constant volume and constant
pressure runs. They both worked out just perfect.
Thanks.
jenk.
--- Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Cenk,
>
> >BOND = 222354.5092
>
> This is HUGE... Your system has obviously blown up.
> Try writing the
> coordinate file every step and then you can watch
> and see what happens.
>
> I suspect that something is very wrong with the
> structure from the constant
> volume simulation. Check this carefully. If you can
> post that output file
> that would be helpful as well. It is possible that
> your initial system was
> highly compressed and so as soon as you remove the
> constraints of being
> fixed to a certain volume it expanded extremely
> rapidly (i.e. an explosion).
> This would imply that your initial structure, from
> which you did the
> constant volume simulation, was overly compressed.
> You will need to go back
> and check this.
>
> > imin=0, nstlim=200,
> > dt=0.002, cut=5, irest=1, ntx=7,
>
> Alternatively it could be due to cut=5...!!! Do you
> really mean to use a 5
> angstrom cutoff???
>
> > Group input for restrained neamine
> > 100.0
> > RES 1
> > END
> > END
>
> Your restraints may also be causing you a problem.
> But I would check the
> other things first.
>
> 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 |
>
> Note: Electronic Mail is not secure, has no
> guarantee of delivery, may not
> be read every day, and should not be used for urgent
> or sensitive issues.
>
>
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Received on Fri Jan 28 2005 - 19:53:00 PST
