From: Ropon-Palacios G. (
Date: Sat Aug 07 2021 - 13:52:04 CDT

The hydrogen masses, have the value of 3 amu as corresponds after the distribution, I am using 4 fs with rigidbonds all, (this means and what difference does it have from SETTLE, I do not use settle), the frequencies and nonbonded are 1, And my mistake is just in a hydrogen, which binds to the N that is involved, in patch with the glycosylation, could it be that the mass is not attached to it?


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. 
From: "Geist, Norman" <>
Date: Saturday, August 7, 2021 at 1:43 PM
To: René Hafner TUK <>, "Ropon-Palacios G." <>, vmd-l <>
Subject: Re: vmd-l: Hydrogen mass repartition PSFGen2.0
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.
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
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!. 
Dipl.-Phys. René Hafner
TU Kaiserslautern