From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Sep 17 2010 - 14:19:26 CDT
NAMD would (until I fixed it in August) silently default to "none" of
the given value for rigidBonds was not recognized. Not a problem in this
case, but not the right thing to do either.
On Fri, 3 Sep 2010, Mert Gür wrote:
> Dear Leonardo,
> Thanks a lot.
> I searched in the log file. There is no "RIGID" word in it.
> So I assume the "rigidbonds off" command worked.
> On Fri, Sep 3, 2010 at 9:21 AM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>
>> Dear Mert,
>> On Thu, Sep 2, 2010 at 10:03 PM, Mert Gür <gurmert_at_gmail.com> wrote:
>>> Dear all,
>>> This question is just out of curiosity.
>>> One of my friends did a long MD simulation writing "rigidbonds off" in
>>> the configuration file.
>>> However in the user guide it says that
>>> Acceptable Values: none, water, all
>>> My friends MD simulation have run for a long time.
>>> Does using "rigidbonds off" mean "rigidbonds none"?
>>> If so could I use "off" for any of the "none" values in the configuration
>>> If it does not mean "rigidbonds none" how can I check what it actually
>> Have you looked at the log file? Something like:
>> Info: RIGID BONDS TO HYDROGEN : WATER
>>> I am asking these questions because I am planning to use the resulting
>>> trajectory for further analysis (TMD and SMD).
>> Leonardo Trabuco, Ph.D.
>> CellNetworks, BioQuant
>> University of Heidelberg, Germany
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