AMBER Archive (2003)

Subject: Re: AMBER: more than 100,000 atoms ?

From: David Smith (David.Smith_at_cup.uni-muenchen.de)
Date: Fri Aug 08 2003 - 10:17:39 CDT

Hi all,

Thanks to Tom and Robert for their quick responses.The reason I have
specifically CC'd this to Kristina will become clear shortly.

Actually, I was using tleap and (apparently) I had no problems with this
stage. That is, both the prmtop and crd files have an I6 natom. I didn't
sift through the code to find out why.

The real problem was sander6. I had a look at sander7 (should've done it
before, I know) and now understand (a bit) how it is handled there.

My main problem is that I want to do some PMF calculations on my large
system. I had previously been using GIBBS for these.

I note that gibbs7 still reads I5. I tried to change gibbs6 to read (and
write) I6. That is, I changed the 9018 format line in GETCOR
and MDWRIT in giba.f to FORMAT(I6,5E15.7). This allowed me to start
running (no complaints about number of atoms not matching between prmtop
and crd files) but then I just get zero's for everything (all coords and
energies etc). I admit my programming is not that great so I am a bit
lost as to how to fix that.

If I would like to do my PMF's on the big system, I basically see three
options:

(a) get gibbs6 (or 7) running to read I6.
(b) Use PMEMD in a way similar to what Kristina was doing.
(c) Use Sander 7 in a way similar to what Kristina was doing

The first problem with options b and c is that I don't have any
experience with doing PMFs this way. In this respect, I was wondering if
Kristina could give me a brief description (maybe an example) as to how
it is done and what the WHAM method is all about. Maybe a reference or
something that could lead me in the right direction.

I guess the second problem is whether or not the restraints are working
properly in PMEMD. Therefore, I would really appreciate it if any
developments by Robert and Kristina in this direction could be posted to
the list.

Finally, if anybody has any suggestions as to how to get gibbs running
with I6, I would also immensely appreciate that.

I think I have now spent my adjective database and will politely sign
off.

Thanks to everyone for their patience.

David.

On Thu, 2003-08-07 at 22:33, Robert Duke wrote:
> David -
> Sander 7 can do this, no problems. So can PMEMD, if you are mostly still in
> an amber 6 context. The prmtop is not a problem but your first inpcrd file
> is. Really all that is needed is the change of natom from i5 to i6; if you
> are coming from tleap or xleap, I don't know how it normally handles this.
> I whacked the xleap source to get it to do the right thing, myself, but that
> is not a standard part of the distribution. The change I made is shown by
> the following
> diff (amber 6 source):
> diff -tr ./leap/unitio.c /home/rduke/amber6/src.ori/leap/src/leap/unitio.c
> 5466c5466,5478
> < FortranFormat( 1, "%5d" );
> ---
> > /*
> > * Write a amber 6 inpcrd atoms line for less than 100,000 atoms, and a
> > * amber 7 inpcrd atoms line for 100,000 or more atoms. This allows us to
> > * use PMEMD with more than 99,999 atoms.
> > */
> >
> >
> >
> > if (iVarArrayElementCount(uUnit->vaAtoms) < 100000)
> > FortranFormat( 1, "%5d" );
> > else
> > FortranFormat( 1, "%6d" );
> >
>
> The guys I work with routinely deal with systems of over 100,000 atoms,
> which is one reason I modified sander 6 into pmemd (faster, handles bigger
> problems (up to about 329844 atoms)in less memory). See the amber web page,
> amber.scripps.edu, for the link to get a copy of PMEMD.
>
> Regards - Bob Duke
>
> ----- Original Message -----
> From: "David Smith" <David.Smith_at_cup.uni-muenchen.de>
> To: <amber_at_scripps.edu>
> Sent: Thursday, August 07, 2003 3:44 PM
> Subject: AMBER: more than 100,000 atoms ?
>
>
> > Hi all,
> >
> > Apologies if this question has come up before but I don't remember it
> > and a quick search of the archives didn't net me anything.
> >
> > I wanted to try a system with more than 100,000 atoms. I know it's a bit
> > big but my boss is an ambitious guy.....
> >
> > I gave it a go and initially got very confused by getting caught by
> > "Peek Ewald" in a simple sander minimization.
> >
> > After a bit of surprise and a few write statements I realized that NATOM
> > was being read as "I5" from the CRD file. Changing it to "I6" got me
> > past "Peek Ewald" but I then got stuck a bit later. The web page tells
> > me that, in general, NATOM is "I6" in PARMTOP but "I5" in CRD.
> >
> > I am still "trapped" in Amber 6 but my guess is that these formats
> > persist into Amber 7 ?
> >
> > Can anyone recommend a way to do such a system with AMBER (any version)?
> >
> > i.e. Would I have to change all the formats associated with "read (9,F)"
> > statements. Is there a semi fast way to do it ? Even if I did manage
> > that, would the developers imagine that something else would break and
> > that I should simply abandon the whole idea.
> >
> > Thanks for your patience ....
> >
> > David.
> >
> >
> > --
> > ---------------------------------------
> > Dr. David Smith
> > Department of Chemistry
> > Ludwig Maximilians University
> > Butenandt-Str. 5-13, D-81377 Munich
> > Germany
> > Tel.: +49 (0)89 2180 77740
> > Fax.: +49 (0)89 2180 77738
> > e-mail: David.Smith_at_cup.uni-muenchen.de
> > ---------------------------------------
> >
> >
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>
>
>
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-- 
---------------------------------------
Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Germany
Tel.: +49 (0)89 2180 77740
Fax.: +49 (0)89 2180 77738
e-mail: David.Smith_at_cup.uni-muenchen.de
---------------------------------------

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