From: salehesam_at_gmail.com
Date: Fri Jan 13 2017 - 10:36:41 CST
Christian,
I experienced this once, however the issue for me was that two atoms happen to have overlapped by random chance, causing the energy to reach this somewhat infinite value.
Upon reconstructing the system the error I received had disappeared.
Have you tried reconstructing your system?
Can you replicate the error?
Best,
Saleh Al-Khalifa
> On Jan 13, 2017, at 12:19, Christian Jorgensen <chrisjorg_at_gmail.com> wrote:
>
> 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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