From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Sat Aug 07 2021 - 18:53:39 CDT

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

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