From: Jeff Wereszczynski (jmweresz_at_mccammon.ucsd.edu)
Date: Thu Nov 29 2012 - 16:57:24 CST
Does it work properly with the CPU version? Or is it a problem with
aMD+GB in general? I believe that the only aMD that works on the GPU
is the dihedral acceleration (probably because those calculations are
done on the CPU even in the GPU NAMD).
On Thu, Nov 29, 2012 at 7:39 AM, Felipe Merino <fmerinoleon_at_gmail.com> wrote:
> Dear all,
> I havwe been trying lately to run some accelerated molecular dynamics
> combined with implicit solvent using a cuda version of NAMD 2.9. However,
> when it comes to calculate the dV for the potential energy the
> electrostatics are not calculated correctly.
> ACCELERATED MD: STEP 5000000 dV 174.884 dVAVG 174.884 BOND 217.271 ANGLE
> 514.686 DIHED 785.12 IMPRP 0 ELECT -164.908 VDW -207.159 POTENTIAL 1145.01
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC KINETIC
> TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG
> ENERGY: 5000000 217.2714 514.6861 785.1195 0.0000
> -3943.6178 -165.2773 0.0000 0.0000 813.3220
> -1778.4960 309.5932 -2591.8180 -1768.8754 309.5932
> I guess the program is not considering the solvation energy in the
> Is there any way to correct this?
-- Jeff Wereszczynski Postdoctoral Scholar University of California, San Diego http://mccammon.ucsd.edu/~jwereszc
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