Hi Eugene,
I was a little confused by your email, but I'll try to clarify what I meant
a little. I was concerned that your saveene potential energies do not
match the frames in your reservoir. I used the following procedure to make
my reservoir
1) Run regular MD: write both coords and velocities to trajectory file
2) Post-process trajectory file with sander to get potential energies
3) Grep potential energies out of the sander output to create saveene file
(with appropriate header)
4) Read trajectory file with cpptraj and write out restart files for
reservoir
5) run R-REMD
Good luck,
--Niel
On Fri, Oct 4, 2013 at 5:34 PM, Eugene Yedvabny <eyedvabny.berkeley.edu>wrote:
> Hi Niel,
>
> Thank you for the informative response. After you've mentioned that the
> potential energies do not correspond to the structures, I've ran through my
> REMD mdout files and there are indeed energy discrepancies. For example,
> here's an excerpt from one of the replicas:
>
> ==========================REMD EXCHANGE
> CALCULATION==========================
> Exch= 2 RREMD= 2
> Replica Temp= 442.35 Indx= 24 Rep#= 24 EPot= -14662.13
> Partner Temp= 434.82 Indx= 23 Rep#= 23 EPot= -14769.94
> Metrop= 0.119672E+00 delta= 0.212300E+01 o_scaling= -1.00
> Rand= 0.863800E+00 MyScaling= -1.00 Success= F
> ========================END REMD EXCHANGE
> CALCULATION========================
>
> NSTEP = 500 TIME(PS) = 571.000 TEMP(K) = 454.47 PRESS =
> 0.0
> Etot = -10392.8625 EKtot = 4228.8407 EPtot =
> -14621.7032
> BOND = 35.7788 ANGLE = 90.6779 DIHED =
> 112.9705
> 1-4 NB = 33.1220 1-4 EEL = 91.0480 VDWAALS =
> 2207.4054
> EELEC = -17192.7058 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.5519E-04
> TEMP0 = 442.3500 REPNUM = 24 EXCHANGE# =
> 2
>
> ------------------------------------------------------------------------------
>
> My nptr and nstlim are set to the same value, so exchange calculations and
> energy printing should correspond to the same structure, However, EPot from
> REMD exchange doesn't match EPtot from nptr printout. Are different
> algorithms used to compute the two energies?
>
> I've also ran Sander's analysis mode on that replica's mdcrd, using the
> exact same input file but changing imin=5 and maxcyc=1, and it returned the
> following energy for the first structure:
>
> minimizing coord set # 1
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.4603E+04 1.6780E+01 1.0139E+02 CZ 25
>
> BOND = 38.1245 ANGLE = 85.3875 DIHED =
> 114.1624
> VDWAALS = 2227.6348 EEL = -17191.9287 HBOND =
> 0.0000
> 1-4 VDW = 32.4372 1-4 EEL = 91.2190 RESTRAINT =
> 0.0000
> minimization completed, ENE= -.14602963E+05 RMS= 0.167801E+02
>
>
> My ntwx was set to 2x ntpr, so the first structure in the mdcrd should
> correspond to the 2nd exchange attempt/printout, which is what I provided
> at the top. This energy, however, doesn't matter either of the two EPot
> from the REMD mdout. The energy differences are significant enough that I
> can't disregard them as precision errors. So now I am completely confused
> as to which energy is actually the correct energy of my structure and how
> to go about creating my reservoirs.
>
> Any help would be much appreciated!
>
> Thank you,
> Eugene Yedvabny
>
>
> On Friday, October 4, 2013 at 1:25 PM, Niel Henriksen wrote:
>
> > Eugene,
> >
> > I don't think there is any "all-in-one" tool to do what you are asking.
> > The multi-step process is what I have used.
> >
> > Unless I misunderstand you, you seem to be using potential energies (from
> > the mdout file) and coordinate frames from the SAME simulation.
> > Unfortunately, the printed potential energies do not correspond to the
> > written frames in the mdcrd file. (see
> > http://archive.ambermd.org/201308/0199.html ) So you probably need to do
> > the Sander-in-analysis-mode step regardless of what your plans are.
> >
> > --Niel
> >
> >
> > On Fri, Oct 4, 2013 at 12:50 PM, Eugene Yedvabny <eyedvabny.berkeley.edu(mailto:
> eyedvabny.berkeley.edu)>wrote:
> >
> > > Hello Amber community,
> > >
> > > Is there any functionality in cpptraj or ptraj that enables easy
> reservoir
> > > generation and energy calculation to use in pmemd REMD with -rremd 2?
> > > Currently I am generating my reservoirs by parsing through mdout files
> and
> > > extracting EPtot values, followed by manually creating the header with
> the
> > > random seed. This is of course doable, if a little cumbersome when
> > > extracting energies from several MD runs into one reservoir. But my
> current
> > > project involves slightly modifying some of the force-field
> parameters, and
> > > I would need to recalculate the energies of my reservoir structures
> using
> > > this new prmtop. It seems the only way to do so presently would be to
> run
> > > Sander in analysis mode on all of my trajectories and then parse out
> the
> > > generated mdouts into another reservoir.
> > >
> > > Since ccptraj can load many mdcrds and prmtops, it would be ideal to
> have
> > > a function that generates the reservoirs and savene files all in one
> go,
> > > akin to clusterdihedral function that is used for -rremd 3.
> Unfortunately I
> > > was not able to find a reference to any such function, or any function
> in
> > > cpptraj that would generate EPtot values for all mdcrd frames. Does
> anyone
> > > have a suggestions, or is my present multi-step process the only way
> to go
> > > about generating the reservoir?
> > >
> > > Thank you,
> > > Eugene Yedvabny
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org (mailto:AMBER.ambermd.org)
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
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> >
> >
>
>
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Received on Sun Oct 06 2013 - 21:30:04 PDT
