AMBER Archive (2003)

Subject: Re: AMBER: PMEMD and EAMBER

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Aug 07 2003 - 16:06:11 CDT

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