Re: Does "rigidbond off" work instead of "rigidbonds none"

From: Mert Gür (gurmert_at_gmail.com)
Date: Fri Sep 17 2010 - 14:44:14 CDT

Ok,
Thanks Jim. Now I can be sure.
Best,
mert

On Fri, Sep 17, 2010 at 10:19 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> 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.
>
> -Jim
>
>
> 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.
>> Best,
>> Mert
>>
>> On Fri, Sep 3, 2010 at 9:21 AM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>
>> wrote:
>>
>>> 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
>>>>
>>> file?
>>
>>> If it does not mean "rigidbonds none" how can I check what it actually
>>>>
>>> did?
>>
>>>
>>> Have you looked at the log file? Something like:
>>>
>>> Info: RIGID BONDS TO HYDROGEN : WATER
>>> (...)
>>>
>>> Cheers,
>>> Leo
>>>
>>> I am asking these questions because I am planning to use the resulting
>>>> trajectory for further analysis (TMD and SMD).
>>>>
>>>> Best,
>>>> Mert
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Leonardo Trabuco, Ph.D.
>>> CellNetworks, BioQuant
>>> University of Heidelberg, Germany
>>>
>>>

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