Re: amber-developers: updated "to-do" list for amber8

From: Robert Duke <>
Date: Thu, 13 Nov 2003 19:52:06 -0700

David -
Glad to hear you want PMEMD in 8.0. This is definitely okay with me, and
also believe Lee will be very pleased, though I have not recently
it with him. I will be glad to do the updates listed; I may need a few
suggestions but believe I should be able to do the code. I will need to
look back at your schedules, but since I run PMEMD dev relatively
independently, I don't think we should have any problems with things being
available when they are needed. As you know, we have the 3.1 drop of
in place; I actually have two other cuts, done recently. One drops the
non-CIT code paths (which mostly supported amber 6 style polarization and
few little-used options), should we want to put polarizable ff code in
at some point in time; Tom D. and I have not really discussed this, but it
is a possibility that we could relatively quickly have polarizable ff's in
pmemd version. The other is a development base for experimentation on
electrostatics schemes (obviously not going anywhere soon). Anyway, I
be glad to do the enhancements, and we can discuss other things as folks
Regards - Bob

----- Original Message -----
From: "David A. Case" <>
To: <>
Sent: Thursday, November 13, 2003 9:30 PM
Subject: Re: amber-developers: updated "to-do" list for amber8

> On Thu, Nov 13, 2003, Robert Duke wrote:
> > Any update on how you guys are feeling about PMEMD? Want it to remain
> > of the product in the 8 timeframe? Any specific requests?
> Sorry. PMEMD was not on the June, 2003 "to-do" list, so I did not
> anything about it in my latest e-mail. That was an oversight on my
> My intent is to include PMEMD officially in the amber8 release, so that
> everyone will have it. I'm assuming (from earlier e-mails) that this
> be OK with you and with Lee, and that we/you can adapt your release
> to become a chapter in the Users' Manual (I'm happy to work on that.)
> PMEMD is clearly useful to amber users, whether or not NAMD might be
> on some machine or other. There is a whole new learning curve for NAMD,
> which can be avoided by using PMEMD, which has minimal differences with
> sander code people are already familiar with. And there appear to be
> of (pretty common) machines where PMEMD is much faster than NAMD.
> As for "specific requests": the modifications that seem to be to have
> greatest potential benefit are these:
> (1) The integrators in runmd.f have been updated (yet again!). The new
> is actually simpler than the old, but has better temperature regulation
> options. It would be nice if PMEMD could incorporate this, so that
> trajectories with sander8 and PMEMD could continue to be compeltely
> equivalent. (I'm willing to work on this, either by directly modifying
> or by providing advice.)
> (2) The thermodynamic integration capability of sander is another key
> where users could benefit from faster simulations that have better
> scaling. I know that you thought about this a few months ago, and
> that there were some complications (which is correct), but I don't think
> are really major ones.
> (3) There is a new "DUMPFREQ" (dump frequency) parameter in sander8 that
> provides an avenue for users to create potentials of mean force from
> sampling (and similar calculations). Implementing this in PMEMD should
> involve a few lines of code, and would allow users to transfer the PMF
> instructions from sander (which will be in the new users' manual)
> into PMEMD.
> Of course, the above depends on your time and interests, and are only
> as ideas to think about. I know you have mentioned other things (new
> electrostatics, merging the cit and non-cit code, etc.), and it's hard
> plans when funding is uncertain. I'm willing to help with certain
> and certainly to put in my two cents, but it's clearly up to you and Lee
> make the "real" decisions.
> Hope this helps clarify things. Apologies again for leaving out the
> of PMEMD in the previous e-mail.
> ..dac
> --
> ==================================================================
> David A. Case | e-mail:
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA |
> ==================================================================
Received on Wed Apr 05 2006 - 23:50:07 PDT
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