From: Hadi Dinpajooh (dinpajooh_at_gmail.com)
Date: Tue Aug 05 2014 - 11:52:44 CDT
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."
Sent from my iPhone
> On Aug 5, 2014, at 7:54 AM, Kenno Vanommeslaeghe <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.
> 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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