From: Jeff Wereszczynski (jwereszc_at_iit.edu)
Date: Wed Jun 18 2014 - 13:14:11 CDT
Hi Thomas,
Yes, in theory you can still go ahead and use these for reweighing if the
aMD code isn't taking into account the LJCorrection energy. Its analogous
to only boosting the dihedrals and not the total potential energy.
Cheers,
Jeff
Jeff Wereszczynski
Assistant Professor of Physics
Illinois Institute of Technology
http://www.iit.edu/~jwereszc
On Wed, Jun 18, 2014 at 6:20 AM, Thomas Evangelidis <tevang3_at_gmail.com>
wrote:
> Greetings,
>
> My query is a possible problem of the aMD implementation in NAMD 2.10
> (CVS-2013-11-09) in the case of explicit solvent simulation with the AMBER
> ff. In the 2011 paper about the aMD implementation, CHARMM ff was used.
> However, in order to use an AMBER ff in NAMD I have to switch on the
> LJcorrection. In that case the vdW and Potential energies printed in the
> "ACCELERATED MD:" line are different from those in the "ENERGY:" line. In
> contrast, when I switch off the LJcorrection flag all the energies are
> identical. Have a look at some sample lines:
>
>
> with LJcorrection on:
>
> ACCELERATED MD: STEP 87543000 dV 72.2669 dVAVG 82.8525 BOND 5288.23 ANGLE
> 18672.4 DIHED 16735.6 IMPRP 0 ELECT -204303 VDW 15665.3 POTENTIAL -147940
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
> ENERGY: 87543000 5288.2277 18672.4165 16735.6300
> 0.0000 -204302.7087 13520.8743 0.0000 1.6135
> 47684.6230 -102399.3237 311.5958 -150083.9467
> -102080.5748 311.3023 -259.4794 -246.9799
> 738674.3246 -29.1724 -29.0266
>
> with LJcorrection off:
>
> ACCELERATED MD: STEP 87543000 dV 76.7961 dVAVG 94.015 BOND 5120.57 ANGLE
> 18918.2 DIHED 16759.4 IMPRP 0 ELECT -204135 VDW 15280.7 POTENTIAL -148058
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
> ENERGY: 87543000 5120.5713 18918.1941 16759.3518
> 0.0000 -204135.4881 15280.7398 0.0000 -1.3280
> 47291.1523 -100766.8069 309.0247 -148057.9592
> -100448.3863 309.6632 -155.2256 -154.3696
> 726366.2601 -22.7045 -22.6922
>
>
> Apparently the analytical tail correction is not considered in dV
> calculation, which results to a moderate overestimation of the potential
> energy and consequently to a lower boost, which is not bad. Do you reckon I
> can still use these dV values for reweighting? I don't see any problem
> using them, just wanted to have the expert opinion of a more experienced
> user/developer.
>
>
> thanks in advance,
> Thomas
>
>
>
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