From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Aug 05 2014 - 15:00:49 CDT
Rereading my own post, I realize I might have written it too
CHARMM-centric, as the CHARMM program defaults to Nosé-Hoover and
Anderson-Hoover for NVT and NPT, respectively, so CHARMM users don't
really have a good reason to use Langevin Dynamics except for the purposes
I listed.
I'm now starting to wonder what the recommended protocol would be to
perform an NPT simulation with rigidBonds in NAMD without resorting to
Berendsen's weak coupling algorithm, which would be plain wrong for the
2-phase system Viswanath Pasumarthi (the person who originally asked the
question last week) is seeking to study.
Or perhaps the information in the resource I linked to is outdated, and
the Langevin equations needed to produce the correct velocity distribution
with rigidBonds have since been added to NAMD? I *vaguely* remember having
simulated Langevin with rigidBonds at some point without any problems...
On 08/05/2014 02:41 PM, Kenno Vanommeslaeghe wrote:
> That doesn't mean the model wouldn't be rigid, just that the temperature
> wouldn't be right. More importantly, I don't think the person who asked
> the original question is planning to perform Langevin integration.
> Langevin is good to mimic the effects of solvent collisions when running
> implicit solvent and can also be used to improve sampling in some
> instances, bit it wouldn't be very appropriate for his purpose. The gold
> standard for explicit solvent simulations with CHARMM is Verlet (and
> that's also what was used to parametrize the force field).
>
> On 08/05/2014 12:52 PM, Hadi Dinpajooh wrote:
>> Well, as mentioned in the link NAMD is not well developed if one uses
>> rigid models and Langevin integration:
>>
>> " ... Although /NAMD/ will run with Langevin integration and rigid bonds
>> both active, the equilibrium temperature of the system does not converge
>> to the correct value. Different Langevin equations are needed to produce
>> the correct velocity distribution, which have not yet been added to
>> /NAMD/."
>>
>> Hadi
>>
>> Sent from my iPhone
>>
>> On Aug 5, 2014, at 7:54 AM, Kenno Vanommeslaeghe
>> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>>
>>> On 08/05/2014 03:14 AM, Hadi wrote:
>>>> (2) It is my understanding that the parameters you copy-pasted into
>>>> your e-mail are just "reasonable values" for in case an MD engine or
>>>> methodology is used that does not support rigid water. They won't give
>>>> the exact same properties as the true rigid TIP3P model. NAMD,
>>>> however, does support rigid water; assuming the psf is generated
>>>> correctly, all one need to do is put the following line in the NAMD
>>>> input:
>>>> rigidBonds water
>>>> Though if you're using the CHARMM force field, it's actually
>>>> recommended to instead use
>>>> rigidBonds all
>>>> because that's what the force field is parametrized for.
>>>>
>>>>
>>>> I hope it is clear that unlike MC simulations, a rigid model can actually
>>>> be slightly flexible in MD simulations.
>>>>
>>>> Hadi
>>>
>>> Umm no, provided that no mistakes were made in the set-up of SHAKE
>>> (rigidBonds in NAMD), a rigid model is really rigid in MD. Except for
>>> insignificant numerical deviations related to the SHAKE tolerance. More
>>> info here: http://www.ks.uiuc.edu/Research/namd/1.5/ug/node64.html
>>>
>
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