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

From: MEHRAN MB (mb.mehran1_at_gmail.com)
Date: Tue Apr 01 2014 - 21:44:36 CDT

Dear J,

As Ivan kindly replied to your email, you can find your answer in NAMD user
guide,
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node33.html
if you do not understand the description, you may want to check Wrap
explanation in NAMD tutorials:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node9.html

wrapping & unwrapping :
there is no difference in physics and it would just change the way of
demonstration. (you can find more by searching in namd-l )

Hope it helps,

Mehran

On Wed, Mar 19, 2014 at 10:38 PM, Research Jubilant <
research.jubilant_at_gmail.com> wrote:

> 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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