AMBER Archive (2007)

Subject: Re: AMBER: MD simulation error

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jul 25 2007 - 12:41:42 CDT

well you can change your ntwx to write less often, but you
should check and see why you are exceeding your quota.
do you have lots of files that should be compressed or moved
to long term storage? this isn't an amber issue.

don't use bad simulations (too big a time step) to make up for
technical issues with computers....

On 7/25/07, Lili Peng <lilipeng_at_gmail.com> wrote:
>
> Thank you Drs. Case and Walker for your insightful comments. The only
> reason why I have a large timestep is that I initially tried it with dt=
> 0.001, but I get the error:
>
> "forrt1: Disk quota exceeded.
> forrt1: severe (38) error during write, unit 12, file
> /users/lpeng/md_classical10000.mdcrd"
>
> I wonder if this has anything to do with Amber (my guess is a no). I'm
> accessing AMBER via SDSC's Teragrid machine, and I presume that it's because
> of my disk space on the SDSC server. Any thoughts?
>
> Thanks again,
> Lili
>
> On 7/24/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> >
> > Hi Lili,
> >
> > Most probably it is to do with time step - you are suing a 5fs time step
> > and while you fix all bonds (ntf=3, ntc=3) this is still likely too large -
> > take a look at your trajectory file and see what it looks like. Note I don't
> > think ntf>2 is used much so you may want to check that it actually works
> > properly for your system - is there a reason why you want to keep all the
> > bonds fixed? You should note that most things have not been parameterized to
> > run in this mode so I would be very cautious of your results - make sure you
> > can prove that your choice to keep the bonds fixed is justified - I.e.
> > perhaps try this out on some model systems and show that you can recover the
> > same results for the entity you are interested in whether you fix all bonds
> > or just bonds to hydrogen.
> >
> > You also have an extremely large gamma_ln value.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | 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.
> >
> >
> > ------------------------------
> > *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> > Behalf Of *Lili Peng
> > *Sent:* Tuesday, July 24, 2007 16:54
> > *To:* amber_at_scripps.edu
> > *Subject:* AMBER: MD simulation error
> >
> > Dear all,
> >
> > I am getting the following error for my MD simulation:
> >
> > Coordinate resetting (SHAKE) cannot be accomplished, deviation
> > is too large
> >
> >
> > NITER, NIT, LL, I and J are : 0 1 7 16 28
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> >
> >
> > My input file is the following:
> >
> > 310K constant temp MD
> > &cntrl
> > imin=0, ntb=1,
> > cut=8.0, ntc=3, ntf=3,
> > tempi=310.0, temp0=310.0,
> > ntt=3, gamma_ln=50,
> > nstlim=10000, dt= 0.005,
> > ntpr=1, ntwx=1,
> > /
> >
> > Does anyone have any idea why this occurs? Does it have anything to do
> > with the timestep?
> >
> > Thank you for your time,
> > Lili
> >
> >
>

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