From: Christian Jorgensen (chrisjorg_at_gmail.com)
Date: Fri Jan 13 2017 - 10:19:03 CST
Hello,
I am running an energy minimization on a membrane protein
prepared using Drude Prepper.
I can run the normal psf/pdb prior to turning it into Drude psf/pdb.
I am unable to run the first minimization with Drude on, as the energy at
step 0 is inf
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME
PRESSAVG GPRESSAVG DRUDECOM DRUDEBOND DRCOMAVG
DRBONDAVG
ENERGY: 0 6915.9918 23501.9638 34656.5055
251.6123 9999999999.9999 31402.7078 0.0000 0.0000
9999999999.9999 9999999999.9999 9999999999.9999 9999999999.9999
9999999999.9999 9999999999.9999 9999999999.9999 9999999999.9999
1000000.0000 9999999999.9999 9999999999.9999 9999999999.9999
9999999999.9999 9999999999.9999 9999999999.9999
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU -nan -nan DUDX -nan -nan -nan
As said, this Drude psf/pdb structures come from an equilibrated structure.
I think the problem is with the placing of the Drude lone pairs.
Has anyone experienced this?
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