VMD-L Mailing List

From: Georcki Ropon (groponp_at_gmail.com)
Date: Sat Aug 07 2021 - 11:55:41 CDT

Thank so much Rene!!

Geo.

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De: René Hafner TUK <hamburge_at_physik.uni-kl.de>
Enviado: Saturday, August 7, 2021 4:20:23 AM
Para: Ropon-Palacios G. <groponp_at_gmail.com>; vmd-l <vmd-l_at_ks.uiuc.edu>
Asunto: Re: vmd-l: Hydrogen mass repartition PSFGen2.0

Hi Geo,

    When using HMR you need to apply rigidBonds to water only. The whole point of repartitioning masses is to reduce fast oscillations frequencies (of hydrogen bonds) you would not allow before due to rigidBonds and with HMR let them oscilliate less fast (which allows higher timestep).

Kind regards

René

On 8/6/2021 8:52 PM, Ropon-Palacios G. wrote:

Dear user,

I’m using HMR for a protein with glycosilation (N-glycosilation), make HMR using function implement into psfgen 2.0,

I’ve check rigth patch but when run md simulation (minimization, equlibration good), get error in rattle algorithm to an hydrogen atoms into atom N involved into glycosilation, as can fix it?

Please help me!.

Best,

Geo. 

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Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany