From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Tue Sep 10 2013 - 10:57:23 CDT
Please keep the messages on the list. I can only reply to the list.
There is most likely some very strange charge assignments in your protein or that like charges are sitting close together. CI2 isn't that big of a protein so it should be trivial to look at the atomic charge assignments and do some long minimizations and save the snapshots from these long minimization steps to look for deformations in the protein backbone or wild swings of sidechains.
From: dayanidhi mohanta [mailto:512cy1009_at_nitrkl.ac.in]
Sent: Monday, September 09, 2013 10:01 PM
To: Bennion, Brian
Subject: Re: namd-l: RE: VDW energy is negative but total energy is positive
yes there is CI2 in the box
i have sent the plots for pure methanol minimization and the minimization of CI2 in 100% methanol
----- Original Message -----
From: "Brian Bennion" <Bennion1_at_llnl.gov>
Sent: Monday, September 9, 2013 8:55:53 PM
Subject: namd-l: RE: VDW energy is negative but total energy is positive
Is there something else in the methanol box? A protein, DNA? Methanol should not contain an improper term.
More importantly is the fact that your electrostatic term is huge for just a methanol box. That is what is driving the positive energy.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of dayanidhi mohanta
Sent: Friday, September 06, 2013 9:19 PM
Subject: 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
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