Hi Bob,
Just an update here:
Setting ntb=0 and igb=0 in Amber selects a gas phase simulation using the
direct space nonbond routines from the code that would normally be used for
ewald/pme. This is seen in the output as:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
So there is nothing illegal with this input option you get a gas phase
simulation with no periodic boundaries and a pair list that is heuristically
updated. This is compared to setting igb=6 which will also give you a gas
phase simulation but in this case will go through the GB portion of the code
instead of the ewald portion of the code. The essential difference here is
that no non-bond list is used and the cut off criteria is evaluated on every
step. For a small gas phase system (<300 atoms or so) this can be a little
bit faster than the igb=0 version. Although in reality it is really meant
only for testing.
Short summary: This is unrelated to the "could not find cntrl namelist
error."
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Robert Duke
> Sent: Tuesday, July 10, 2007 14:58
> To: amber.scripps.edu
> Subject: Re: AMBER: Could not find cntrl namelist
>
> Okay, I looked at this and saw no funny nonprinting special
> chars. What I
> did see is a nonperiodic system (ntb = 0) with a PME
> simulation (igb = 0),
> and no &ewald section. Now, pme does a periodic boundary
> condition by
> default, but you can get a barebones vacuum simulation by
> specifying in an
> &ewald namelist a value for eedmeth of 4 (bare coulomb) or 5
> (distance-dependent dielectric). I sort of suspect, without
> looking at the
> sander code, that there is a bug in input parsing that maybe
> is incorrectly
> identifying this illegal combination of inputs, and producing
> the wrong
> error message. This is a quick guess; I have not looked back
> at the sander
> code (don't know which version anyway) and this is a nonissue
> with PMEMD
> because I don't support non-generalized Born vacuum
> simulations at present.
> I would first try sticking
> &ewald
> eedmeth=4,
> /
> after the &cntrl and see if that works. Sorry if I am off on
> this, but
> thought a quick comment couldn't hurt much. These comments
> are based on
> amber 9; probably true for 8 and 7 also.
> Best Regards - Bob Duke
>
> ----- Original Message -----
> From: "Francesco Pietra" <chiendarret.yahoo.com>
> To: <amber.scripps.edu>
> Sent: Tuesday, July 10, 2007 5:11 PM
> Subject: RE: AMBER: Could not find cntrl namelist
>
>
> > Hi Ross:
> > I'll study your suggestions below, which arrived when I had
> decided to
> > simplify
> > the problem by running equatorial methylcyclohexane,
> prepared for xleap
> > with
> > antechamber. The same issue "Could not find cntrl namelost" arose.
> >
> > This time, contrary to all previous experience, I could
> quit the xleap
> > window
> > without getting the "not saved" message. Contrary to my
> hope, it didn't
> > anticipate the solution.
> >
> > I also run my eqeq molecule with different mdin, always
> getting the "Could
> > not
> > ..." error message.
> >
> > Attached are all relevant files.
> >
> > Thanks
> >
> > francesco pietra
> >
> >
> >
> >
> > --- Ross Walker <ross.rosswalker.co.uk> wrote:
> >
> >> Hi Francesco,
> >>
> >> > What I fear at this point is related to what I posted
> >> > yesterday about a remind
> >> > by David Case that antechamber treats single residues:
> >>
> >> The issue is that the only possible things that could be
> generating this
> >> error message is either there is something wrong with the
> mdin file, the
> >> incorrect file was specified with -i or there is some
> issue with read
> >> permissions of the mdin file. At this point in the code
> the prmtop file
> >> hasn't even been opened so it cannot be related to a
> problem with that.
> >>
> >> Could you please attach your mdin file to an email (as an actual
> >> attachment)
> >> direct from the copy on the machine on which you are
> having problems. If
> >> you
> >> have to ftp it to another machine to email it then make
> sure you select
> >> binary format for the transfer. Then we can take a look
> and see if there
> >> is
> >> something weird going on.
> >>
> >> Another option you could try as well is to create a brand
> new file on the
> >> machine on which you are running sander and explicitly
> type in, on that
> >> machine in vi, everything you want in the input file. That
> way you work
> >> around any kind of weird corruption and/or strange control
> characters
> >> that
> >> may have made it into the old file during the copying /
> cut / pasting
> >> etc.
> >>
> >> Seeing the exact input file as sander sees it on your
> machine will really
> >> help.
> >>
> >> All the best
> >> Ross
> >>
> >> /\
> >> \/
> >> |\oss Walker
> >>
> >> | HPC Consultant and Staff Scientist |
> >> | San Diego Supercomputer Center |
> >> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> >> | http://www.rosswalker.co.uk | PGP Key available on request |
> >>
> >> Note: Electronic Mail is not secure, has no guarantee of
> delivery, may
> >> not
> >> be read every day, and should not be used for urgent or
> sensitive issues.
> >>
> >>
> >>
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> >
> >
> >
> >
> >
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Received on Wed Jul 11 2007 - 06:07:54 PDT
