AMBER Archive (2004)

Subject: Re: AMBER: PMEMD Built ? Wont run..

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Tue May 11 2004 - 14:41:15 CDT

Hi,

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_at_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.
> > Regards - Bob Duke
> >
> > ----- Original Message -----
> > From: "Gary Waters" <gwaters_at_paracel.com>
> > To: <amber_at_scripps.edu>
> > Sent: Tuesday, May 11, 2004 12:00 PM
> > Subject: AMBER: PMEMD Built ? Wont run..
> >
> >
> > > Hi Everyone,
> > >
> > > I believe I built pmemd correctly with mpich.
> > > On mpich I can do some of the example and test runs fine, with no
> > > errors. Then I go over to pmemd and run my script, and get these
> > > errors. I do not know what is going on, can someone shed some light on
> > > my dilemma ?
> > >
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > > unit 5, file /export/bionumerik/pmemd.in
> > > Image PC Routine Line Source
> > > pmemd 0811333F Unknown Unknown Unknown
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