Hi,
I do not run the calculation in my computer, but in a supercomputing
centre, so I have to ask to them if they applied all bugfixes.
I tried to do the same calculation without gpu and it seems to run.
I'll try to put ntpr=1, and then I re-write.
Thank you in advance.
ELisa
2012/6/22 Daniel Roe <daniel.r.roe.gmail.com>
> Hi,
>
> Is this error occurring right away or are some steps able to complete?
> This could indicate some instability in your system. You can re-run
> with ntpr=1 and see exactly at what step the error occurs.
>
> Also, have you applied all the bugfixes?
>
> -Dan
>
> On Fri, Jun 22, 2012 at 6:36 AM, Elisa Frezza <elisa.frezza.gmail.com>
> wrote:
> > Dear all,
> >
> > I am using AMBER 11 with PME and GPU.
> > I simulated a pair of DNA in an octahedral box.
> > The input file that I use is the following
> >
> > run: step 1 MD
> > &cntrl
> > imin = 0,
> > irest = 0 ,
> > ntx = 1,
> > nstlim = 5000, dt = 0.002,
> > ntc = 2 , ntf = 2,
> > ntt = 3, gamma_ln = 2.0,
> > ntp=1, taup=1,
> > pres0=1,
> > tempi = 100.0, temp0 =100.0,
> > ntb = 2 ,
> > ntpr = 250 , ntwx = 250, ntwr = 500 ,
> > cut = 9,
> > ioutfm = 1
> > ntr=1
> > /
> > &end
> > Keep DNA fixed with weak restraints
> > 1000.0
> > RES 1 136
> > END
> > END
> >
> > and I occur this error. I tried to change the value of the cutoff, but I
> > have still this error.
> >
> > | ERROR: max pairlist cutoff must be less than unit cell max sphere
> > radius!
> >
> > Thank you in advance
> >
> > Elisa
> >
> > --
> > Elisa Frezza
> > Ph.D. Student in Materials Science and Engineering
> > Dipartimento di Scienze Chimiche
> > Università di Padova
> > via Marzolo, 1
> > 35131 Padova - Italy
> > Phone: +39 049 827 5149
> > Skype: elisa.frezza
> > Emai: elisa.frezza.gmail.com
> > elisa.frezza.studenti.unipd.it
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Lab Specialist
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.frezza.gmail.com
elisa.frezza.studenti.unipd.it
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Received on Fri Jun 22 2012 - 06:30:04 PDT
