From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Sep 09 2013 - 01:14:20 CDT
Hi,
I don't know why you suppose this to be a problem. Who says that total energy needs to be positive if VDW is negative? The biggest part of the total energy in your system is the potential energy, so in sum your total energy is positive of course. If you want to know if your minimization was sufficient, plot the total energy and see if it has converged (VMD->NAMD Plot). Additionally, your question is not really NAMD related, but about understanding molecular dynamics simulations themselves, therefore try to understand what theory is behind the simulation, regardless of NAMD.
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von dayanidhi mohanta
> Gesendet: Samstag, 7. September 2013 06:19
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: VDW energy is negative but total energy is positive
>
> Sir, i am new to NAMD and I'm using NAMD_2.9_Linux-x86_64-TCP/namd2.
> Sir, i have run the minimization of a methanol box (of dimension 60A:
> pdb file was generated using PACKMOL and the psf file using PSFGEN) for
> 50000 steps using NAMD. my output files show that VDW energy is
> negative where as the total energy is positive. Sir, i would like to
> know if there is some problem with my system.
>
> I'm attaching the output of the 50000th step for your kind reference
>
>
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL
> TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 50000 921.1493 571.4178 277.3650
> 6.8703 17646.8329 -8080.5121 0.0000 0.0000
> 0.0000 11343.1231 0.0000 11343.1231 11343.1231
> 0.0000 -2425.3588 -2425.4013 216000.0000 -2425.3588
> -2425.4013
>
> Thanking You in advance
>
> Dayanidhi Mohanta
> PhD (Chemistry)
> NIT Rourkela
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