AccelMD + GBIS

From: Felipe Merino (fmerinoleon_at_gmail.com)
Date: Thu Nov 29 2012 - 09:39:18 CST

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
calculation.

Is there any way to correct this?

Regards

Felipe

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:19 CST