From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Tue Aug 12 2014 - 14:11:40 CDT
> On 08/12/2014 01:19 PM, Viswanath Pasumarthi wrote:
>> Moving on, as Maxim suggested, on checking the variation of length of
>> O-H
>> bond with force constants, kb = 1,2,5,10,100,450, the bond lengths
>> varied
>> from 5% to 15% on average for 10 randomly selected bonds. This only
>> reinforces the failure of rigidBonds all constraint.
>
> Yes, it does.
As Alex previously pointed out, the variations reported for O-H bond
length are corresponding to the minimization stage. More importantly, I
have observed that the deviations for the same O-H bond length during MD
step are in the order of 10^-4, implying rigidBonds constraint working.
Please correct me if I'm wrong, for some reason since NAMD doesn't support
constrained minimization, these distortions are possible during
minimization and for this reason, it is necessary to specify bond and
angle force constants in the parameter file despite having rigidBonds
constraint active.
>
>> But the second
>> warning message posted above indicates that NAMD identified water as a
>> rigid molecule.
>
> It's not as simple as NAMD "identifying water as a rigid molecule" and
> everything being good and fine from there onward. NAMD internally has to
> define 3 constraints per water molecule in order for it to be rigidified
> properly, and the process of defining these constraints is somewhat
> convoluted from an end-user's perspective, involving bond and angle
> entries in the psf as well as the parameter file. Messages are issued at
> different stages in the process of NAMD reading files and starting an MD
> run, and since these different stages operate on different parts of the
> data, said messages may seem inconsistent to a non-expert.
>
> I cannot make sense out of the information you provided so far; some
> critical parts are missing, and it seems possible that not everything you
> posted is from the same run. Please attach *full* inputs (.in , .psf ,
> .prm ) that would allow someone to reproduce the problem.
>
>
The full input files are available at
https://www.dropbox.com/sh/knfhvxhbo3o3nis/AADND5IrZXOmkLqRfaWOlNSka.
Please give your comments on which information is missing.
Thank you.
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