Re: inconsistence in NAMD and AMBER energy

From: Yi Shang (mirandaisbest_at_gmail.com)
Date: Tue Jul 21 2009 - 10:22:45 CDT

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>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
> >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>
> > > > To: 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:
> > > > 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:
> > > > &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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:14 CST