AMBER Archive (2005)

Subject: RE: AMBER: Error: vlimit exceeded for step

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jun 06 2005 - 18:24:21 CDT


I suspect your cap force is set wrong. What version of Amber are you using?
Have you applied the bugfixes?

Check the values of IVCAP and FCAP from your output file. In Amber 8 the
default is 0 for ivcap which is what you want assuming that you created the
prmtop file in xleap using the solvatecap command. For fcap the default is
1.5 which is normally reasonable. Check what yours is. For older versions of
Amber the default may be 0.0.

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Hwankyu Lee
> Sent: 06 June 2005 15:47
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Error: vlimit exceeded for step
>
> When I looked at the beginning and end trajectories in VMD, I
> could see
> that water box around solutes looks bigger with increasing time. It
> looks like system size slowly and continuously blows up and then
> finally crashed around 580ps, although my system has reasonable
> temperature.
> Could you tell me how to solve this problem?
>
> Hwankyu.
>
> On Jun 6, 2005, at 1:19 PM, Ross Walker wrote:
>
> > Dear Hwankyu,
> >
> >> vlimit exceeded for step 93807 ; vmax =
> >> 23.91630977621595
> >> vlimit exceeded for step 93808 ; vmax =
> >> 40.75498760131579
> >>
> >> Coordinate resetting cannot be accomplished,
> >> deviation is too large
> >> iter_cnt, my_bond_idx, i and j are : 3 1 5140 5139
> >
> > It is strange that you see this error after 580ps. Although your
> > system may
> > have been unstable for a while before this and eventually blows up.
> > Your
> > temperature in the output you give looks good as well. I
> take it all
> > the
> > amber8 test cases pass on your machine.
> >
> > Can you zoom in around the time when things go wrong? I.e. Run from
> > say 450
> > -> 580ps with ntwx=1 so that you can carefully watch things in vmd.
> > Then you
> > can see where it starts to blow up from. This might make
> the problem
> > easier
> > to identify.
> >
> > I am sorry I can't help much more than that.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Department of Molecular Biology TPC15 |
> > | The Scripps Research Institute |
> > | Tel:- +1 858 784 8889 | EMail:- ross_at_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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>
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