VMD-L Mailing List

From: Geist, Norman (norman.geist_at_uni-greifswald.de)
Date: Sat Aug 07 2021 - 15:17:34 CDT

Rigidbonds has limitations, with HMR it allows a timestep of 4fs,
otherwise only 2fs. Sry for being short, but am typing on the phone
right now.

Am Samstag, den 07-08-2021 um 21:14 schrieb René Hafner TUK:

 

Hi Norman,

    what would the phyiscal meaning of HMR be, if we keep all
non-solvent bonds rigid anyway?

Best

René

On 8/7/2021 8:43 PM, Geist, Norman wrote:

 No, you should keep rigid bonds to all. What timestep do you use?
Have you checked the PSF contains rescaled masses? (easy to see on
hydrogen atoms having a mass of 3)

Im using it for all my simulation without any problems. Don't scale
the water, only solute.

Bests
Norman Geist

Am Samstag, den 07-08-2021 um 11:20 schrieb René Hafner TUK:

 

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.

 

 

 -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany

 

 -- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany