AMBER Archive (2003)

Subject: Re: Fw: AMBER: PMEMD and EAMBER

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Aug 11 2003 - 08:49:36 CDT

David -
At the moment at least, PMEMD does not support "free energies using
thermodynamic integration". David Case once mused that he might try adding
that functionality to PMEMD in order to better understand the code. I
really don't know how serious he was or what his potential timeframe was.
Personally, like everybody else, I have about a thousand things going on,
and have been more focused on performance as opposed to adding
functionality. If there is a loud enough clamor and it would not take too
much effort, I could probably be persuaded to do it (hence the cc to the
mailing list), especially if some folks in my group decide they could use
the functionality also. Thanks for the positive comments!
Regards - Bob
----- Original Message -----
From: "David Smith" <David.Smith_at_cup.uni-muenchen.de>
To: "Robert Duke" <rduke_at_email.unc.edu>
Sent: Monday, August 11, 2003 5:00 AM
Subject: Re: Fw: AMBER: PMEMD and EAMBER

> Bob,
>
> Thanks very much for the bug fix. I will probably play around with it in
> the next few days. It seems that most of my calculations do have the
> potential to work in this framework.
>
> I was just wondering (although I am guessing that the answer is no) if
> there is any chance to use something like "Free energies using
> thermodynamic integration" (p107 in AMBER7 manual) with PMEMD ?
>
> Thanks again for your answer.
>
> All the best.
>
> David.
>
> PS. I, for one, really appreciate the effort you put into this project.
>
>
>
> On Fri, 2003-08-08 at 21:15, Robert Duke wrote:
> > David -
> > I am forwarding you a copy of the mail I sent to Kristina because it
> > includes the attachment that is the fix for pmemd nmr restraint
energies. I
> > sent this to the amber reflector, but it probably got filtered out due
to
> > the attachment. Don't know if you want the fix or not, but at least
this
> > way it will be easy if you do.
> > Regards - Bob
> >
> > ----- Original Message -----
> > From: "Robert Duke" <rduke_at_email.unc.edu>
> > To: "Kristina Furse" <kristina.e.furse_at_vanderbilt.edu>
> > Cc: <amber_at_scripps.edu>
> > Sent: Friday, August 08, 2003 2:13 PM
> > Subject: Re: AMBER: PMEMD and EAMBER
> >
> >
> > > Kristina -
> > >
> > > I got a chance to look at your example runs and the pmemd code this
> > morning,
> > > and it is actually really a simple problem. I reordered some code in
> > > force_cit.f90 in an effort to make things a little more clear, and
screwed
> > > up in regard to when ene(1) gets updated if nmropt is nonzero. The
simple
> > > one line fix to src.pmemd/pmemd/force_cit.f90 is:
> > > 664a665
> > > > ene(1) = ene(1) + enmr(1) + enmr(2) + enmr(3)
> > >
> > > I have also attached the modified version of force_cit.f90 for your
> > > convenience, though that may give folks on the amber reflector grief.
> > >
> > > I am virtually certain this fixes the problem, but if you would
rebuild,
> > > test it, and let me know, I would appreciate it. Normally, I like to
test
> > > stuff myself, but this one was dead easy, if you don't mind rebuilding
and
> > > testing yourself, I think that would be best. Sorry for messing it
up.
> > At
> > > one point in time, I had actually removed support for nmropt == 1 from
> > > pmemd, since I was not sure how the coordinate and forces distribution
> > > issues were going to play out there. I ended up re-including it when
I
> > > determined that it could be done relatively easily, and our
temperature
> > > scaling tests worked. If everyone would check nmropt== 1 results
> > carefully,
> > > though, I would appreciate it. I simply don't have test coverage of
the
> > > gazillion different possible options. I would note that in my perusal
of
> > > the original amber 6 code, I noticed that pme breaks nmropt==1- based
> > > modification of cut, so I don't even trust that all of this stuff
still
> > > works in amber 6 (could be thats the only problem, but if you don't
have a
> > > complete test suite, you DON'T KNOW).
> > >
> > > I expect that in the next week or so I will include this fix in a new
drop
> > > of pmemd that also includes support for the various alphaservers and
the
> > > cray t3e at PSC.
> > >
> > > Regards - Bob
> > >
> > > ----- Original Message -----
> > > From: "Kristina Furse" <kristina.e.furse_at_vanderbilt.edu>
> > > To: "Robert Duke" <rduke_at_email.unc.edu>
> > > Sent: Friday, August 08, 2003 1:21 PM
> > > Subject: RE: AMBER: PMEMD and EAMBER
> > >
> > >
> > > > Thank you so much! My system is pretty big--104,234 atoms. If that
> > sounds
> > > like
> > > > too much trouble to work with, I could do a quick test with a
smaller
> > > system
> > > > and send that. If not, I'll ship the big guy.
> > > >
> > > > Kristina
> > > >
> > > > >===== Original Message From "Robert Duke" <rduke_at_email.unc.edu>
=====
> > > > >Kristina -
> > > > >It is very possible that something (like an enmr) got whacked in
the
> > > pmemd
> > > > >code work without getting noticed. The nmropt == 1 stuff is not
> > > extensively
> > > > >tested; we mostly use the temperature stepping capabilities in our
> > group.
> > > > >Non-nmr constraints were tested and do work (hb benchmark),
producing
> > the
> > > > >same results for sander 6, 7, pmemd, and pmemd 7-compatibility
mode.
> > If
> > > you
> > > > >will send me your input (gzipped, please) I will be glad to track
down
> > > and
> > > > >fix the bug. I'll do this for any nmropt == 1 stuff folks turn up;
I
> > have
> > > > >tried to not touch the nmropt == 1 code because of the testing
impact,
> > > but
> > > > >it is always possible that something obscure got missed.
> > > > >Regards - Bob
> > > > >----- Original Message -----
> > > > >From: "Kristina Furse" <kristina.e.furse_at_vanderbilt.edu>
> > > > >To: <amber_at_scripps.edu>
> > > > >Sent: Thursday, August 07, 2003 4:32 PM
> > > > >Subject: AMBER: PMEMD and EAMBER
> > > > >
> > > > >
> > > > >> Hello-
> > > > >>
> > > > >> We've been trying out PMEMD, using it for some potential of mean
> > force
> > > > >> calculations (using NMR-style torsional constraints to bias the
> > > sampling,
> > > > >then
> > > > >> a WHAM method to get the PMF curve).
> > > > >>
> > > > >> I ran some initial test runs to compare pmemd with sander in
AMBER7
> > > > >(running
> > > > >> on an SGI origin). While comparing the test runs, I noticed
something
> > > > >about
> > > > >> the computation of EAMBER in minimization and dynamics output
> > (below).
> > > > >Looking
> > > > >> at the first step of minimization output for the very same input
> > > > >coordinates
> > > > >> run in sander (amber7) and pmemd (amber7_compat=1), the energies
are
> > > > >identical
> > > > >> (well, to be exact, EEL is different by 0.0001) except for
EAMBER,
> > > which
> > > > >is
> > > > >> off by 2.5778kcal, which is exactly the restraint energy minus
the
> > > 0.0001.
> > > > >I
> > > > >> summed the energies by hand and it looks like PMEMD may be
> > subtracting
> > > the
> > > > >> restraint energy twice, or else not including it in the total
> > potential
> > > > >energy
> > > > >> calculation then still subtracting it to get EAMBER?
> > > > >>
> > > > >> I took a look at some dynamics output (same input coordinates as
> > > before)
> > > > >from
> > > > >> sander7 and pmemd, and I think the same thing may be going on
there.
> > > For
> > > > >> pmemd, it seems like the number for EPtot already does not
include
> > > > >restraint
> > > > >> energy, then EAMBER has restraint energy subtracted again.
> > > > >>
> > > > >> Has anyone else noticed this? Did I miss something somewhere, or
am I
> > > just
> > > > >> adding wrong...
> > > > >>
> > > > >> Thanks!
> > > > >>
> > > > >> Kristina
> > > > >>
> > > > >>
> > > > >>
> > > > >> Minimization output:
> > > > >>
> > > > >> Sander (amber 7):
> > > > >>
> > > > >> NSTEP ENERGY RMS GMAX NAME
> > > NUMBER
> > > > >> 1 -3.5193E+05 1.6203E+01 1.3187E+02 CD
> > > 17121
> > > > >>
> > > > >> BOND = 3402.1061 ANGLE = 9311.0284 DIHED =
> > > > >11245.0567
> > > > >> VDWAALS = 48314.8917 EEL = -472531.9934 HBOND =
> > > > >0.0000
> > > > >> 1-4 VDW = 4345.3096 1-4 EEL = 43982.3959 RESTRAINT =
> > > > >2.5779
> > > > >> EAMBER = -351931.2050
> > > > >>
> > > >
> > >
> >
>===========================================================================
> > > =
> > > > >==
> > > > >> =
> > > > >> NMR restraints for step 1
> > > > >> Energy (this step): Bond = 2.578 Angle = 0.000
Torsion =
> > > > >0.000
> > > > >> Energy (tot. run) : Bond = 2.578 Angle = 0.000
Torsion =
> > > > >0.000
> > > > >>
> > > > >> DEVIATIONS: Target=(r2+r3)/2 Target = closer
of
> > > r2/r3
> > > > >> This step Entire run This step
> > Entire
> > > > >run
> > > > >> ave. rms ave. rms ave. rms
ave.
> > > > >rms
> > > > >> Bond 0.253 0.254 0.253 0.254 0.253 0.254
> > 0.253
> > > > >0.254
> > > > >> Angle 0.000 0.000 0.000 0.000 0.000 0.000
> > 0.000
> > > > >0.000
> > > > >> Torsion 0.000 0.000 0.000 0.000 0.000 0.000
> > 0.000
> > > > >0.000
> > > > >>
> > > >
> > >
> >
>===========================================================================
> > > =
> > > > >==
> > > > >> =
> > > > >>
> > > > >>
> > > > >>
> > > > >>
> > > > >> PMEMD (amber7_compat=1):
> > > > >>
> > > > >> NSTEP ENERGY RMS GMAX NAME
> > > NUMBER
> > > > >> 1 -3.5193E+05 1.6203E+01 1.3187E+02 CD
> > > 17121
> > > > >>
> > > > >> BOND = 3402.1061 ANGLE = 9311.0284 DIHED =
> > > > >11245.0567
> > > > >> VDWAALS = 48314.8917 EEL = -472531.9933 HBOND =
> > > > >0.0000
> > > > >> 1-4 VDW = 4345.3096 1-4 EEL = 43982.3959 RESTRAINT =
> > > > >2.5779
> > > > >> EAMBER = -351933.7828
> > > > >>
> > > >
> > >
> >
>===========================================================================
> > > =
> > > > >==
> > > > >> =
> > > > >> NMR restraints for step 1
> > > > >> Energy (this step): Bond = 2.578 Angle = 0.000
Torsion =
> > > > >0.000
> > > > >> Energy (tot. run) : Bond = 2.578 Angle = 0.000
Torsion =
> > > > >0.000
> > > > >>
> > > > >> DEVIATIONS: Target=(r2+r3)/2 Target = closer
of
> > > r2/r3
> > > > >> This step Entire run This step
> > Entire
> > > > >run
> > > > >> ave. rms ave. rms ave. rms
ave.
> > > > >rms
> > > > >> Bond 0.253 0.254 0.253 0.254 0.253 0.254
> > 0.253
> > > > >0.254
> > > > >> Angle 0.000 0.000 0.000 0.000 0.000 0.000
> > 0.000
> > > > >0.000
> > > > >> Torsion 0.000 0.000 0.000 0.000 0.000 0.000
> > 0.000
> > > > >0.000
> > > > >>
> > > >
> > >
> >
>===========================================================================
> > > =
> > > > >==
> > > > >> =
> > > > >>
> > > > >>
> > > > >>
> > > > >> Molecular Dynamics Output:
> > > > >>
> > > > >> Sander (amber7)
> > > > >>
> > > > >> NSTEP = 100 TIME(PS) = 3150.100 TEMP(K) = 296.72 PRESS =
> > > 32.9
> > > > >> Etot = -287279.7774 EKtot = 64194.7299 EPtot
> > > = -351474.5072
> > > > >> BOND = 3498.2008 ANGLE = 9330.0143 DIHED =
> > > 11174.5893
> > > > >> 1-4 NB = 4342.5808 1-4 EEL = 44008.7977 VDWAALS =
> > > 48274.1435
> > > > >> EELEC = -472109.4246 EHBOND = 0.0000 RESTRAINT =
> > > 6.5909
> > > > >> EAMBER (non-restraint) = -351481.0982
> > > > >> EKCMT = 25330.3166 VIRIAL = 24605.6087 VOLUME =
> > > 1019086.6920
> > > > >> Density =
> > > 1.0541
> > > > >> Ewald error estimate: 0.4495E-04
> > > > >>
> > > > >>
> > > > >>
> > > > >> PMEMD (amber7_compat=1)
> > > > >>
> > > > >> NSTEP = 100 TIME(PS) = 3150.100 TEMP(K) = 296.72 PRESS =
> > > 32.8
> > > > >> Etot = -287292.8061 EKtot = 64195.1417 EPtot
> > > = -351487.9478
> > > > >> BOND = 3498.2009 ANGLE = 9330.0138 DIHED =
> > > 11174.5889
> > > > >> 1-4 NB = 4342.5814 1-4 EEL = 44008.7981 VDWAALS =
> > > 48276.0446
> > > > >> EELEC = -472118.1755 EHBOND = 0.0000 RESTRAINT =
> > > 6.5910
> > > > >> EAMBER (non-restraint) = -351494.5388
> > > > >> EKCMT = 25330.5359 VIRIAL = 24608.2331 VOLUME =
> > > 1019085.5924
> > > > >> Density =
> > > 1.0541
> > > > >> Ewald error estimate: 0.4460E-04
> > > > >>
> > > > >>
> > > > >>
> > > > >> **In case you wonder about the difference in restraint energies,
the
> > > > >dynamics
> > > > >> runs have NMR-style constraints on the torsion we're driving, as
well
> > > as a
> > > > >> "virtual bond" to a heme group accomplished using an NMR-style
> > distance
> > > > >> constraint. The minimizations just have the virtual bond.
> > > > >>
> > > > >>
> > > > >>
> > > > >>
> > > > >> Finally, for good measure, dynamics input files:
> > > > >>
> > > > >>
> > > > >> sander (amber7)
> > > > >>
> > > > >> Biased PMF: Cox dimer w/radical, explicit water, 9.0 cut
> > > > >> &cntrl
> > > > >>
> > > > >> nmropt = 1,
> > > > >> ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
> > > > >> ntpr = 100, ntwx = 100, ntwv = 0, ntwe = 0,
> > > > >>
> > > > >> ntf = 2, ntb = 2,
> > > > >> cut = 9.0,
> > > > >>
> > > > >> ibelly = 0, ntr = 0,
> > > > >>
> > > > >> imin = 0,
> > > > >> nstlim = 10000,
> > > > >> nscm = 100,
> > > > >> t = 0.0, dt = 0.001,
> > > > >>
> > > > >> temp0 = 298.0, tempi = 298.0,
> > > > >> ig = 71277, heat = 0.0,
> > > > >> ntt = 1,
> > > > >> tautp = 1.0,
> > > > >> vlimit = 20.0,
> > > > >>
> > > > >> ntp = 1, pres0 = 1.0, comp = 44.6,
> > > > >> taup = 1.0,
> > > > >>
> > > > >> ntc = 2, tol = 0.00001, watnam = 'SPC ',
> > > > >>
> > > > >> &end
> > > > >> &ewald
> > > > >>
> > > > >> nbflag = 1, skinnb = 2.0, use_pme = 1,
> > > > >>
> > > > >> &end
> > > > >> &wt type='END' &end
> > > > >> DISANG=tor0.rst
> > > > >>
> > > > >>
> > > > >> pmemd input file just has the additional flag, amber7_compat=1,
> > > > >>
> > > > >> ****************************************************
> > > > >> Kristina E. Furse
> > > > >> Department of Chemistry
> > > > >> Center for Structural Biology
> > > > >> Vanderbilt University
> > > > >> email: kfurse_at_structbio.vanderbilt.edu
> > > > >>
> > > > >>
> > > >
> >
>> -----------------------------------------------------------------------
> > > > >> The AMBER Mail Reflector
> > > > >> To post, send mail to amber_at_scripps.edu
> > > > >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > > > >>
> > > > >>
> > > > >
> > > > >
> > > > >
> > > >
>-----------------------------------------------------------------------
> > > > >The AMBER Mail Reflector
> > > > >To post, send mail to amber_at_scripps.edu
> > > > >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > > >
> > > > ****************************************************
> > > > Kristina E. Furse
> > > > Department of Chemistry
> > > > Center for Structural Biology
> > > > Vanderbilt University
> > > > email: kfurse_at_structbio.vanderbilt.edu
> > > >
> > > >
> > >
> --
> ---------------------------------------
> 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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