VMD-L Mailing List

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Sat Aug 07 2021 - 14:14:49 CDT

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