Re: [AMBER] unexpected "vlimit exceeded for step" error

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 23 Jun 2010 09:46:31 -0700

Hi Cristina,

I took your input files and ran them in serial using sander v11 and the
calculation crashes after 3 steps. Looking at the mdcrd file it is obvious
there is a problem. Take a look at frame0 and frame2 attached. I zoomed in
on the region where the problem occurs. Loading it into VMD it is obvious.
This is what I meant when I said you should set ntwx=1 and then carefully
look at each frame in VMD.

It is clear you have some issue with the parameters here, or something else
strange going on. It may be related to your mutations.

I would start by investigating this.

Good luck,
Ross

> -----Original Message-----
> From: Cristina Sisu [mailto:csds2.cam.ac.uk]
> Sent: Tuesday, June 22, 2010 9:10 AM
> To: Ross Walker
> Subject: Re: [AMBER] unexpected "vlimit exceeded for step" error
>
> Hi Ross,
>
> If I use a dt=0.001 and an ntlim=100 steps everything is fine for the
> first simulation. If I take the rst file and use it as starting point
> for the next simulation, the problem appears on step 60,
> time(ps)=0.160.
> If I have a larger ntlim = 500 steps, the problem appears at step 120.
> If I use a different dt=0.002 then I start getting problems at step 3,
> time(ps) = 0.006. I attach here the parameter and coordinate files as
> well as the mdin files.
> The mutations occured at residue 73.
> This problem appeared recently with a set of 7 mutants, even though the
> very same mutants in complex with an acylated ligand work absolutely
> perfect (mutated a month ago). I wonder if something corrupted in
> anyway the tleap version on my cluster and the prmtop/inpcrd files are
> not reliable any more?
>
> Thank you for all your help,
> Cristina
>
>
> Ross Walker wrote:
> > Hi Cristina,
> >
> >
> >> For the first 100 steps, everything runs smoothly, however when it
> >> reaches 121st step, something happens and the systems stops
> recording
> >> the coordinates.
> >>
> >
> > This seems very strange. Can you try turning off the restraints and
> see what
> > happens. Also did the location of where vlimit error occurred (step
> number)
> > change when you switched to printing every step? If so then this
> suggests
> > deeper problems. Have run the test cases and verified your AMBER
> > installation is working correctly?
> >
> > If you can send me your prmtop, inpcrd and mdin files (by a direct
> email,
> > not to the list) I will try running it here and see if I can
> reproduce the
> > problem.
> >
> > All the best
> > Ross
> >
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery,
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> > be read every day, and should not be used for urgent or sensitive
> issues.
> >
> >
> >
> >
> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >



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frame2.jpg
(image/jpeg attachment: frame2.jpg)

frame0.jpg
(image/jpeg attachment: frame0.jpg)

Received on Wed Jun 23 2010 - 10:00:05 PDT
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