Re: vmd-l: Re: wrapping option in namd

From: Research Jubilant (research.jubilant_at_gmail.com)
Date: Wed Mar 19 2014 - 22:38:16 CDT

Thanks for the suggestions. That's the first place I always go to every
time I have a question about namd commands. I couldn't understand from
those two repeated sentences given under wrapWater and wrapAll.

J

On Wed, Mar 19, 2014 at 9:58 PM, Ivan Gregoretti <ivangreg_at_gmail.com> wrote:

> Hi Ju,
>
> I think the the best answer is in the user guide:
> http://www.ks.uiuc.edu/Research/namd/2.9/ug/node33.html
>
>
> There is also an online search tool that allows you to find answers in
> NAMD's user guide:
> https://www-s.ks.uiuc.edu/Research/namd/
>
> For answers that can't be found in the manual, don't hesitate to ask.
>
> Cheers,
>
> Ivan
>
>
>
>
>
> Ivan Gregoretti, PhD
> Bioinformatics
>
>
> On Wed, Mar 19, 2014 at 10:34 PM, Research Jubilant <
> research.jubilant_at_gmail.com> wrote:
>
>> Hello all,
>>
>> I have a question about using "wrapAll" option during a simulation. I
>> have this option on in my simulation. What does it really mean? Should I
>> unwrap before I use the generated trajectory in any analyses? I don't see
>> anything strange even if I don't unwrap it.
>> What if I don't use this option?
>>
>> Kindly help me understand the significance of this option. When do I
>> suppose to use this?
>>
>> Ju
>>
>
>

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