Re: [AMBER] rfree: Error decoding variable 1 3 from:

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Thu, 12 Apr 2012 17:05:16 +0200

Dear Professor Case,

Thank you very much. I try to run my input with sander9, but I have still
problems.
I am considering upgrading to Amber12, but now I would like to do some
calculations and tests for my system.
In Amber12, is this input correct?

Thank you very much

Elisa


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,
 restraint_wt=0.05,
 restraintmask=1-48
 /
 &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


2012/4/12 David A Case <case.biomaps.rutgers.edu>

> On Thu, Apr 12, 2012, Jason Swails wrote:
> >
> > >
> > > Note that you could avoid this whole issue of where the group input
> should
> > > be by
> > > using restraint_wt and restraintmask in the &cntrl namelist. (But
> this was
> > > only been implemented in pmemd in Amber11 and later: this is one of
> many
> > > reasons to consider upgrading to Amber12.)
> > >
> >
> > I think it's actually only in pmemd 12, unless it crept into one of the
> > feature upgrades for pmemd.cuda (even more reason to upgrade to 12 :)).
>
> My bad: pmemd11 still requires group input cards.....dac
>
>
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>



-- 
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
UniversitÓ 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 - 08:30:03 PDT
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