Dear Niel,
thank you very much, now it runs.
Next months, I think that I'll upgrade to Amber12 depends on my university.
Elisa
2012/4/12 Niel Henriksen <niel.henriksen.utah.edu>
> Ok, Elisa sent me the input files and I figured it out.
>
> Elisa, this is why I asked you to copy and paste my
> input file directly to your computer and use it.
>
> It's hard to tell in emails, but you have a single space
> in front of each of the following lines of your input file,
> like so:
>
> space
> |
> v
>
> DISANG=dist_chi.RST
> DUMPAVE=restraint.log
> LISTIN=POUT
> LISTOUT=POUT
> &end
> Keep DNA fixed with weak restraints
> 0.05
> RES 1 48
> END
> END
>
> That is enough to confuse pmemd (at least old versions).
> Here is the correct run_md.in file:
>
> run: MD
> &cntrl
> imin = 0, irest = 0 , ntx = 1,
> nstlim = 2500000, dt = 0.002,
> ntc = 2 , ntf = 2,
> ntt = 3, gamma_ln = 2.0,
> tempi = 298.0, temp0 =298.0,
> ntb = 1 ,
> ntpr = 250 , ntwx = 250, ntwr = 500 ,
> cut = 9,
> ig = -1
> ioutfm = 1,
> nmropt=1,
> ntr=1
> /
> &ewald
> nfft1 = 90,
> nfft2 = 90,
> nfft3 = 90,
> /
> &wt type='DUMPFREQ', istep1=1, /
> &wt type='END' /
> DISANG=dist_chi.RST
> DUMPAVE=restraint.log
> LISTIN=POUT
> LISTOUT=POUT
> &end
> Keep DNA fixed with weak restraints
> 0.05
> RES 1 48
> END
> END
>
> Like I said, old versions of pmemd are very finicky.
> This *should* work now, but upgrading to
> amber12 would make your life, and ours, easier =)
> I hope this helps (fingers crossed).
>
> --Niel
>
> Also, Dave's comments about the ewald section still
> apply
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> 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 Thu Apr 12 2012 - 09:00:06 PDT
