From: Christian Jorgensen (chrisjorg_at_gmail.com)
Date: Fri Jan 13 2017 - 11:26:39 CST
Hello, I already set it up twice and got the same error.
I am aware membrane proteins can have randomised setup errors
due to the initial distribution of lipids, which sometimes are not resolved
by the minimizer algorithm.
However, the non-Drude psf/pdb can run fine, with acceptable initial
energies:
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME
PRESSAVG GPRESSAVG
ENERGY: 0 3583.6527 16962.1087 11760.6333
325.3170 -162471.7959 5441.4535 0.0000 0.0000
41673.5090 -82725.1218 309.7646 -124398.6309
-82428.7248 309.7646 267.2281 267.6599
829440.0000 267.2281 267.6599
I will run a longer equilibration and then re-setup the Drude files, but I
am convinced the problem lies with the positioning of the lone pairs.
I will try to reproduce the error again, but as said I redid the setup two
times already.
On Fri, Jan 13, 2017 at 4:36 PM, <salehesam_at_gmail.com> wrote:
> 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?
>
>
>
>
-- --------------------------- Christian Jorgensen PhD student, King's College London ---------------------------
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:01 CST