VMD-L Mailing List

From: Ropon-Palacios G. (groponp_at_gmail.com)
Date: Sat Aug 07 2021 - 19:35:14 CDT

What happens is that for water molecules SETTLE is still used, but when we activate All in rigidBond we do not do it because of the high frequency problem (which can be solved with HMR), but because these atoms still rotate on their atom heavy.

 

I understood it, I hope I am correct.

  

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Ropón-Palacios G. BSc., MSc. 
Computational biophysicist, 
Associate Research, 
Laboratorio de Modelagem Computacional, 
Departamento de Ciências Exatas, 
Universidad Federal de Alfenas, Minas Gerais, Brasil. 
Phone: +51 935 055240. 
E-mail: groponp_at_gmail.com. 
 
 
 
 
 
From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of René Hafner TUK <hamburge_at_physik.uni-kl.de>
Date: Saturday, August 7, 2021 at 7:31 PM
To: vmd-l <vmd-l_at_ks.uiuc.edu>
Cc: "Gumbart, JC" <gumbart_at_physics.gatech.edu>
Subject: Re: vmd-l: Hydrogen mass repartition PSFGen2.0
 
Dear JC,
 may you step in here? :)
   Though do I now understand correctly that:
            HMR can solve the limitations of the RATTLE algorithm (involving masses and not working good enough with low masses like hydrogen masses and timesteps >2fs),
        but the oscillations frequencies of hydrogen bonds (non solvent) would still be too high to be captured correctly and we therefore need "rigidBonds all"?
Best
René
On 8/7/2021 10:17 PM, Geist, Norman wrote:
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. 
 
 
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Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany
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Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany