AMBER Archive (2004)

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

From: Gary Waters (gwaters_at_paracel.com)
Date: Tue May 11 2004 - 15:08:49 CDT

Hi ,

I went through, and through trial and error, I found that these
3 parameters were causing problems. I am just not sure why.

ntcm, nt, dtemp

The ndfmin does not seem to cause problems, but I will find out
more when the run completes.

Thanks for the input guys,

-Gary Waters

On Tue, 2004-05-11 at 12:41, Scott Brozell wrote:
> 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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-- 
Gary Waters
Product Support Specialist
Paracel Inc. 
1055 E. Colorado Blvd. 
Pasadena, CA 91106 
gary.waters_at_paracel.com
Office:  626-744-2046 
Fax:     626-744-2001
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