From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Aug 12 2014 - 13:31:04 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.
> 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.
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