Ok, I think the issue was due to different application of constraints
between the two integrators. Turning of constraints for both programs leads
to the expected agreement.
We just purchased a boat load of GPUs, so we will be trying this out soon
enough.
On Wed, Mar 18, 2015 at 11:13 AM, Brian Radak <brian.radak.accts.gmail.com>
wrote:
> Ah yes, I forgot to turn on RATTLE in NAMD. I had already set ntf = 2 in
> AMBER. Even so, the energies are a bit different:
>
> NAMD w/RATTLE "all": BOND = 277.4616
> AMBER (ntf=2) : BOND = 272.9150
>
> By mdin is *very* minimal:
>
> &cntrl
> nstlim=0, igb=6, ntf=2
> /
>
> Anything else?
>
>
> On Wed, Mar 18, 2015 at 11:03 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Wed, 2015-03-18 at 10:54 -0500, Brian Radak wrote:
>> > Here is the output from NAMD with the input PSF/PDB and from AMBER with
>> the
>> > output PARM7/RST7. This is just a dipeptide in vacuum with 999. cutoff
>> and
>> > no switching/shifting. The potential energies are in bold.
>> >
>> > ETITLE: TS BOND ANGLE DIHED
>> IMPRP
>> > ELECT VDW BOUNDARY MISC
>> > KINETIC
>> > TOTAL TEMP POTENTIAL TOTAL3
>> > TEMPAVG
>> > ENERGY: 0 296.7573 68.9638 10.7652
>> > 0.8898
>> > -82.0083 296.9008 0.0000 0.0000
>> > 0.0000
>> > 592.2686 0.0000 *592.2686* 602.4975
>> > 0.0000
>> >
>> >
>> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
>> > = 0.0
>> > Etot = 568.4243 EKtot = 0.0000 EPtot
>> > = *568.4243*
>> > BOND = 272.9150 ANGLE = 42.2312 DIHED =
>> > 10.5283
>> > UB = 26.7326 IMP = 0.8898 CMAP
>> > = 0.2369
>> > 1-4 NB = 181.3726 1-4 EEL = 32.7326 VDWAALS =
>> > 115.5281
>> > EELEC = -114.7428 EGB = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > Upon closer inspection the following make sense:
>> >
>> > NAMD TERMS : AMBER TERMS
>> > -------------------------------------------------
>> > ELECT = 1-4EEL + EELEC
>> > -82.0083 ~= 32.7326 -114.7428 = -82.0102
>> >
>> > VDW = 1-4 NB + VDWAALS
>> > 296.9008 ~= 181.3726 + 115.5281 = 296.9007
>> >
>> > ANGLE = ANGLE + UB
>> > 68.9638 = 42.2312 + 26.7326 = 68.9638
>> >
>> > DIHED = DIHED + CMAP
>> > 10.7652 = 10.5283 + 0.2369 = 10.7652
>> >
>> > IMPRP = IMP
>> > 0.8898 = 0.8898
>> >
>> > But the bonded energies don't match:
>> > 296.7573 != 272.9150
>> >
>> > I'm not really sure what to do with that.
>>
>> Is ntf=2?
>>
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Brian Radak
> Postdoctoral Scholar
> University of Chicago
> Department of Biochemistry & Molecular Biology
> Gordon Center for Integrative Science, W323A
> 929 E. 57th St.
> Chicago, IL 60637-1454
> Tel: 773/834-2812
> e-mail: radak.uchicago.edu
>
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Wed Mar 18 2015 - 10:00:02 PDT
