Re: inconsistence in NAMD and AMBER energy: AMBER truncted octahedron

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Tue Jul 21 2009 - 11:30:35 CDT

Thanks Vlad,
This differs a bit from info in Chap 3.2 Gromacs manual but appears to be
consistent (up to a rotation or something) and Gromacs uses only 3 sig digits
IN THE MANUAL s.t. 4/9 sqrt(3 ) = 0.770

It's been a long time since I tried this.. does the trajectory
appear "normal" in in VMD, i.e. truncated oct or w/ cells angles of
72/109/72?

TOm

On Tuesday 21 July 2009, Vlad Cojocaru wrote:
> Tom, Yi,
>
> The correct vectors to run periodic simulations with amber-generated
> truncated octahedrons in NAMD are:
> d, 0, 0
> (-1/3)*d, (2/3)sqrt2*d, 0
> (-1/3)*d, (-1/3)sqrt2*d, (-1/3)sqrt6*d
>
> where d is the cell dimension. The volume of the amber truncated
> octahedron is 0.7698*d^3 (from amber code)
> If you use these vectors it should work.
>
> Cheers
> Vlad
>
> Yi Shang wrote:
> > Hi Thomas,
> > I thought about this before.
> > It's true you could get very precise cell dimensions to fit your
> > truncated octahedron. But there is no discriminance in NAMD that could
> > tell if that's a octahedron or a box (no angle parameters, for
> > example). It only takes three dimension parameters and assumes it's a
> > box.
> >
> > So, personally I don't think any imaging methods other than box would
> > work with NAMD. Basically we could not restart amber simulation in
> > truncated octahedron, rerun it with periodic box instead...
> >
> > On Tue, Jul 21, 2009 at 11:14 AM, Thomas C. Bishop <bishop_at_tulane.edu
> > <mailto:bishop_at_tulane.edu>> wrote:
> >
> > The important take home message is as you say.
> >
> > "And I suggest all people that are or want to do NAMD using AMBER
> > parameters
> > need to keep in mind that VDW energy is NOT going to be the same
> > if you are
> > using periodic boundary and NAMD 2.7b1, or older version."
> >
> > w/r/t periodic BC's ( i'm doing this from memory) but I thought
> > that even w/
> > PBC on I could get the same answer up to tyhe VDW issue. NOTE I
> > never figured out how to get truncated octahedron to work ( the gromacs
> > manual has
> > a nice list of how to convert cell dimensions for various
> > geometries) but I
> > thought a cubic cell worked.
> >
> >
> > Tom
> >
> > On Tuesday 21 July 2009, Yi Shang wrote:
> > > Hi all,
> > > Thank you for replying.
> > > Thomas, are you using periodic boundary condition or not? Because
> > > if you look at my email. The energy gap is there only if I use
> > > periodic boundary condition. I was not using any SHAKE, temperature
> > > or
> >
> > pressure
> >
> > > control.
> > > Goutham, I am using same amber parameter file for both
> >
> > simulations when I
> >
> > > did comparison, so I believe force parameters are the same.
> > >
> > > Floris, you are right, by turning of vdw correction in amber
> >
> > simulation
> >
> > > (vdwmeth = 0), I get following energies, notice that vdw energy
> >
> > is exactly
> >
> > > the same as NAMD!! now all energies are consistent...
> > > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00
> >
> > PRESS =
> >
> > > 0.0
> > > Etot = -57081.5138 EKtot = 0.0000 EPtot =
> > > -57081.5138
> > > BOND = 341.5077 ANGLE = 716.0017 DIHED =
> > > 2372.7669
> > > 1-4 NB = 1076.3715 1-4 EEL = 9100.8801 VDWAALS =
> > > 6132.6047
> > > EELEC = -76821.6464 EHBOND = 0.0000 RESTRAINT =
> > > 0.0000
> > > Ewald error estimate: 0.2976E-03
> > > Now I need to think about how to get away with it. And I suggest
> >
> > all people
> >
> > > that are or want to do NAMD using AMBER parameters need to keep
> >
> > in mind
> >
> > > that VDW energy is NOT going to be the same if you are using
> >
> > periodic
> >
> > > boundary and NAMD 2.7b1, or older version.
> > >
> > > On Tue, Jul 21, 2009 at 10:33 AM, Thomas C. Bishop
> >
> > <bishop_at_tulane.edu <mailto:bishop_at_tulane.edu>>wrote:
> > > > I have been able to obtain the exact same energies from NAMD
> >
> > and amber
> >
> > > > for several time steps using suggested parameters in the NAMD
> >
> > manual.
> >
> > > > For this it is easiest to start with a temperature of 0 but
> >
> > you can also
> >
> > > > read
> > > > in a velocity file s.t. they have same coords AND momentum
> > > >
> > > > Obviously you have to turn off anything that relies on random
> >
> > number
> >
> > > > generator
> > > > so NVE it primary target here.
> > > >
> > > > bonds, angle, dihedrals, improper agree w/out any problem
> > > >
> > > > vdw and and elec are tricky.
> > > > first start with a simple cut-off to make sure your parameters
> > > > are consistent.
> > > > then turn on long range interactions. PAY CAREFUL ATTENTION TO
> >
> > NAMD
> >
> > > > SWITCHING
> > > > OPTIONS! see manual on swithcing functions too. This
> >
> > introduces a shift
> >
> > > > in the elec and vdw terms that will make it look like NAMD and
> >
> > AMBER are
> >
> > > > radically different but in terms of forces they are nearly
> >
> > same. make
> >
> > > > switching agree and energies agree also.
> > > >
> > > > finally amber includes a long range vdw correction that will
> >
> > affect the
> >
> > > > trajectory over time but in first few steps ~10 this is
> >
> > minimal. W/
> >
> > > > cutoff they should give almost same result for much longer
> > > >
> > > > Please post what you finally come up w/
> > > >
> > > > Tom
> > > >
> > > > On Tuesday 21 July 2009, Floris Buelens wrote:
> > > > > Hi,
> > > > >
> > > > > I'm not sure about exactly how AMBER handles this issue, but
> >
> > I suspect
> >
> > > > the
> > > >
> > > > > difference might arise from the neglect of van der Waals
> >
> > interactions
> >
> > > > > beyond the cutoff. I think AMBER applies an analytical
> >
> > correction by
> >
> > > > > default for these interactions (search the manual for
> >
> > 'vdwmeth'), while
> >
> > > > > NAMD as of 2.7b1 doesn't yet. I would suggest re-running
> >
> > your analysis
> >
> > > > > using an increasing series of cutoff values, I think you
> >
> > should see the
> >
> > > > > NAMD value converging towards that of AMBER. Alternatively,
> >
> > the option
> >
> > > > for
> > > >
> > > > > analytical corrections for long-range van der Waals has now
> >
> > been added
> >
> > > > > to the latest development code, which you can access through
> >
> > CVS as
> >
> > > > described
> > > >
> > > > > on the NAMD website, if you use that code with the option
> >
> > "LJCorrection
> >
> > > > on"
> > > >
> > > > > I hope you shouldn't see such a big discrepancy. Best wishes,
> > > > >
> > > > > Floris
> > > > >
> > > > >
> > > > > ________________________________
> > > > > From: Yi Shang <mirandaisbest_at_gmail.com
> >
> > <mailto:mirandaisbest_at_gmail.com>>
> >
> > > > > To: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> > > > > Sent: Tuesday, 21 July, 2009 1:31:47
> > > > > Subject: namd-l: inconsistence in NAMD and AMBER energy
> > > > >
> > > > >
> > > > > Hi all,
> > > > > I did some comparison of energy calculated by NAMD 2.7b1 and
> >
> > AMBER 10.
> >
> > > > > I found something intriguing. During simulation, VDW energy
> >
> > from AMBER
> >
> > > > > simulation is constantly much lower from NAMD. So I tried to
> >
> > compare
> >
> > > > point
> > > >
> > > > > energy first. I turned off SHAKE, temperature, and pressure
> >
> > control and
> >
> > > > > only looked at basic energy calculation of one single
> >
> > structure:
> > > > > bonds, angles, dihedrals, electrostatic, and vdw energies. For
> > > > > non-periodic boundary, I had no problem, energies are
> >
> > exactly the same.
> >
> > > > > For periodic boundary condition here comes the problem:
> > > > > -electro energy off by ~14kcal/mol, which is ok, parameters
> >
> > might not
> >
> > > > > be identical in two methods. -vdw energy off by > 600
> >
> > kcal/mol. That's
> >
> > > > > terrible.
> > > > >
> > > > > I tested these inputs on two different periodic systems, and
> >
> > I get the
> >
> > > > same
> > > >
> > > > > result (same energy gap). So I don't think it's system specific
> > > > > problem. Here is my inputs and outputs from one system's
> >
> > comparison (I
> >
> > > > > combined AMBER VDWAALS and 1-4 NB energies to compare to
> >
> > NAMD vdw
> >
> > > > > energy, likewise for electrostatic interaction):
> > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > > > NAMD config.in <http://config.in/>:
> > > > > amber on
> > > > > parmfile box.top
> > > > > ambercoor box.crd
> > > > > binaryoutput no
> > > > > outputname md6
> > > > > outputpressure 1
> > > > > outputenergies 1
> > > > > exclude scaled1-4
> > > > > 1-4scaling 0.83333
> > > > > timestep 2
> > > > > temperature 0
> > > > > cutoff 8
> > > > > switching off
> > > > > PME yes
> > > > > PMEGridSpacing 1.0
> > > > > cellbasisvector1 79.6614 0 0
> > > > > cellbasisvector2 0 60.2065 0
> > > > > cellbasisvector3 0 0 63.7403
> > > > > cellorigin 0 0 0
> > > > > run 0
> > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > > > amber md.in <http://md.in/>:
> > > > > &cntrl
> > > > > imin = 0, nstlim = 1, dt = 0.002,
> > > > > irest = 0, ntx = 1,
> > > > > tempi = 0.0, temp0 = 0.0,
> > > > > ntwx = 0, ntwe = 0, ntwr = 0, ntpr = 1,
> > > > > cut = 8.0,
> > > > > /
> > > > >
> > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > > > namd energies:
> > > > > ETITLE: TS BOND ANGLE DIHED
> > > >
> > > > IMPRP
> > > >
> > > > > ELECT VDW BOUNDARY
> > > > > MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3
> > > > > TEMPAVG PRESSURE GPRESSURE VOL UME
> > > > > PRESSAVG GPRESSAVG
> > > > > ENERGY: 0 341.5078 716.0018 2372.7673
> > > >
> > > > 0.0000
> > > >
> > > > > -67739.0356 7208.9795 0.0000
> >
> > 0.0000 0.0000
> >
> > > > > -57099.7791 0.0000 -57099.7791 -56529.2524
> > > >
> > > > 0.0000
> > > >
> > > > > 11740.3005 -276.1608 305707.0 250
> >
> > 11740.3005
> >
> > > > > -276.1608
> > > > >
> > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > > > amber energies:
> > > > > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) =
> >
> > 0.00 PRESS =
> >
> > > > > 0.0 Etot = -57686.8091 EKtot = 0.0000 EPtot
> >
> > =
> >
> > > > > -57686.8091 BOND = 341.5077 ANGLE =
> >
> > 716.0017 DIHED
> >
> > > > =
> > > >
> > > > > 2372.7669 1-4 NB = 1076.3715 1-4 EEL =
> > > > > 9100.8801 VDWAALS = 5527.3094 EELEC = -76821.6464
> > > > > EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error
> > > > > estimate:
> >
> > 0.2976E-03
> >
> > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > > >
> > > > > It's strange because in NAMD seems most important parameter
> >
> > I would
> >
> > > > > play around with VDW energy is switching, and it's turned
> >
> > off. Same
> >
> > > > > cutoff is set in two inputs, but still, I get very different
> >
> > results.
> >
> > > > > any
> > > >
> > > > suggestions
> > > >
> > > > > would be appreciated! Thanks!
> > > >
> > > > --
> > > > **********************
> > > > Thomas C. Bishop *
> > > > Office: 504-862-3370 *
> > > > Fax: 504-862-8392 *
> > > > **********************
> >
> > --
> > **********************
> > Thomas C. Bishop *
> > Office: 504-862-3370 *
> > Fax: 504-862-8392 *
> > **********************
> >
> >
> >
> >
> > --
> > Miranda

-- 
**********************
Thomas C. Bishop     *
Office: 504-862-3370 *
Fax:    504-862-8392 *
**********************

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