From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Sat Aug 07 2021 - 15:21:21 CDT

Hi Ropon,

    check the supplemental of this paper
    https://urldefense.com/v3/__https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.9b00160__;!!DZ3fjg!q-sAnanz2O5Coy87RYRyi8X7Zj4_-r4Jt5ENpR_fMh5XOUM5OrjwQ0NPXU6XHe2S1w$ .

    https://urldefense.com/v3/__https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.9b00160/suppl_file/ct9b00160_si_002.txt__;!!DZ3fjg!q-sAnanz2O5Coy87RYRyi8X7Zj4_-r4Jt5ENpR_fMh5XOUM5OrjwQ0NPXU7wgUBJBQ$

      But as always, CHECK the output for correctness! :)

    Like the cmd-line tool grep is your friend (or editor of your choice).

Best

René

On 8/7/2021 9:57 PM, Ropon-Palacios G. wrote:
>
> Can share me tcl script for make right HMR , please.
>
> --
>
> *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 <mailto: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 2:50 PM
> *To: *"Geist, Norman" <norman.geist_at_uni-greifswald.de>, vmd-l
> <vmd-l_at_ks.uiuc.edu>
> *Subject: *Re: vmd-l: Hydrogen mass repartition PSFGen2.0
>
> 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

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