From: Yi Shang (mirandaisbest_at_gmail.com)
Date: Tue Jul 21 2009 - 11:04:18 CDT
Thank you Floris! Yes I think using the new code is the right thing to do.
On Tue, Jul 21, 2009 at 11:57 AM, Floris Buelens
<floris_buelens_at_yahoo.com>wrote:
>
> Hi,
>
> > 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.
>
> the above is correct but I think it's fair to say that for most
> applications the impact will be minimal (mainly you'll see pressure and
> equilibrium density being slightly affected by the choice of cutoff;
> dynamics are actually not affected at constant vollume). But of course
> consistency is a good thing and the solution is to use the latest CVS code
> (or future releases after 2.7b1).
> Best,
>
> Floris
>
>
>
> ________________________________
> From: Yi Shang <mirandaisbest_at_gmail.com>
> To: Thomas C. Bishop <bishop_at_tulane.edu>
> Cc: floris_buelens_at_yahoo.com; gouthambs_at_gmail.com; namd-l_at_ks.uiuc.edu
> Sent: Tuesday, 21 July, 2009 16:56:04
> Subject: Re: namd-l: inconsistence in NAMD and AMBER energy
>
>
> 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 *
> >**********************
> >
>
>
> --
> Miranda
>
>
>
>
>
-- Miranda
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