Re: AccelMD + GBIS

From: Thomas Evangelidis (
Date: Sat Dec 01 2012 - 12:03:53 CST

Hi Thomas,
    I didn't realize that you were using Implicit solvent --- this is
something new
in NAMD (the theory is around for a long time but only very recently it was
added to NAMD). If you look at the VDW energy, they're actually very close ---
within round off errors. The only glaring difference is ELECT. I didn't check
the code yet but I'm almost certain that this difference is purely caused by aMD
reporting the wrong types of the electrostatic energy --- the PME term is not
calculated in implicit solvent simulation but this term is hard-coded into our
aMD energy reporting formula. I think I should have more time to check more
carefully this weekend and either solve the discrepancy or put a note on NAMD

    ps, before it's fixed, this would mean that aMDT (boosting total
potential) is
incompatible with implicit solvent simulation.


On Nov 30, 2012, at 12:22 AM, Thomas Evangelidis wrote:
> Hi Yi,> > Yes, output 1 and 3 are from the same .log file, so are outputs 2 and 4.> That's why I asked you what to trust, the "ACCELERATED MD:" or the> "ENERGY:" line?> > For your convenience I have attached the whole log files. The NAMD version> was CVS-2012-11-19.> > best,> Thomas

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