Re: Kb, Ktheta values for TIP3P water model

From: Axel Kohlmeyer (
Date: Tue Aug 05 2014 - 14:28:04 CDT

On Tue, Aug 5, 2014 at 3:10 PM, Hadi <> wrote:
> Kenno,
> In general, I think it is fair to say that unlike MC simulations, the rigid
> models in MD simulations are only slightly flexible considering the

no. that is an unfair and incorrect statement.

> algorithm, rigid tolerance, time step, etc. that will be used. I have
> plotted the histogram of bond length for a given model with appropriate
> parameters and observed that the distribution of bond length has some small
> deviations from a delta function.

that suggests that you didn't do the MD very well.


> Hadi
> On Tue, Aug 5, 2014 at 11:41 AM, 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
>>> < <>> 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:

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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