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.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.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.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Lili Peng
> *Sent:* Tuesday, July 24, 2007 16:54
> *To:* amber.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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Received on Sun Jul 29 2007 - 06:07:13 PDT
