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
> Universitŕ 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
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> 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)
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Received on Fri Jun 22 2012 - 06:30:03 PDT
