Hi Bob,
On Tue, 11 May 2004, Robert Duke wrote:
> Thanks for picking up ndfmin. We should have probably put a list of
> obsolete variables that would cause grief in the doc... While I agree
with
> you that grep is useful, I am not sure that it reflects well on us to
have
> to recommend grepping the source to figure out what inputs are valid,
> though.
Agreed.
Unfortunately, there wasn't enough time to make the Retired Namelist
Variable appendix and the corresponding code warnings comprehensive
with respect to versions before 7.
I have recently updated that appendix in the amber9 cvs tree,
and I hope that such work will continue in the future.
Scott
> ----- Original Message -----
> From: "Scott Brozell" <sbrozell.scripps.edu>
> To: <amber.scripps.edu>
> Sent: Tuesday, May 11, 2004 3:41 PM
> Subject: Re: AMBER: PMEMD Built ? Wont run..
>
> > Both ntcm and ndfmin were valid cntrl namelist variables in
> > sander6, but neither is valid in sander7 or later.
> >
> > Another application of grep
> > f.g ntcm
> > f.g ndfmin
> > :)
> >
> > Scott Brozell
> >
> > On Tue, 11 May 2004, Gary Waters wrote:
> >
> > > Hi Robert,
> > >
> > > Here is my input file; I did try changing the end to a / to no
avail.
> > >
> > > Protein-Drug, complex: eq. ions+water w/200 ps MD, constant T,P.
> > > &cntrl
> > > imin = 0, ntx = 7, ntpr = 50, ntwx = 500,
> > > ntwe = 25, ntxo = 1,
> > > ntcm = 1, ndfmin = 6, nscm = 100,
> > > ntf = 2,
> > > ntb = 2, ntp = 1, pres0 = 1.0,
> > > ntc = 2, nsnb = 10,
> > > scee = 1.2, dielc = 1.0, scnb = 2.0,
> > > nstlim =100000,
> > > cut = 9.0,
> > > t =255.0, dt =.002,
> > > irest = 1,
> > > tempi = 300.0, temp0 =300., ntt = 1, dtemp = 0.0,
> > > tautp = 1.0, taup = 0.2, comp = 44.6,
> > > ig = 123442, pres0 = 1.0,
> > > nmropt = 0, ntr = 0,
> > > jfastw = 0
> > > &end
> > >
> > > Thanks,
> > > Gary Waters
> > >
> > > On Tue, 2004-05-11 at 10:25, Amber admin wrote:
> > > > From: "Robert Duke"
> > > > To: <amber.scripps.edu>
> > > > Subject: Re: AMBER: PMEMD Built ? Wont run..
> > > > Date: Tue, 11 May 2004 12:08:11 -0400
> > > >
> > > > Gary -
> > > > Looks like an invalid variable in the namelist. What are the
contents
> of
> > > > pmemd.in? Are all the variables things read by pmemd? Which
version
> of
> > > > pmemd are you using? There can also be problems with the namelist
> > > > terminator on some systems, and variation in what f77 vs. f90 vs.
f95
> > > > consider valid input. Thus some fortrans expect termination with
> &end,
> > > > others with /, and there can be different requirements for
comments in
> the
> > > > namelists (you have to read the compiler manual). Here though, I
> think you
> > > > just have an invalid variable name.
Received on Wed Apr 05 2006 - 23:50:02 PDT
