Sorry for the delay,
You're right, nativecontacts will return the absolute minimum imaged
distance, not ignoring the self image, which of course is not what you
want. This is something I'm going to have to implement. There is of
course the tedious (but scriptable) alternative where you use the
'image' command to create 26 offset trajectories in each box vector
direction (with xoffset etc) and calculate distances that way, but I
will work on getting a better command into cpptraj in the meantime.
-Dan
On Wed, Jun 4, 2014 at 8:06 AM, newamber list <newamberlist.gmail.com> wrote:
> Hi
>
> I can re-frame my query if it was not so clear.
>
> thanks
>
>
> On Mon, Jun 2, 2014 at 4:36 PM, newamber list <newamberlist.gmail.com>
> wrote:
>
>> Hi Daniel
>>
>>
>> Thanks. I used this command:
>> nativecontacts :1-356 mindist out mindist.dat
>>
>> But I have following doubts:
>>
>> 1) Manual says 'nativecontacts' needs a reference structure so that it
>> would mean I need to update reference structure (reference would be the
>> same as the frame to be analysed) but in case of distance calculation why
>> one would need that?
>>
>> 2) Also am always getting 0.96 as mindist which I think is the distance of
>> hydrogen bonded to some atom (of structure in the unit cell). but I am
>> interested in knowing distances of atom pairs with image rather in the unit
>> cell itself.
>>
>>
>>
>>
>>
>>
>> On Mon, Jun 2, 2014 at 3:50 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>>> Hi,
>>>
>>> You can use the new 'nativecontacts' command in cpptraj with the
>>> 'mindist' keyword to calculate the minimum distance seen either within
>>> a single group of atoms or between two groups of atoms. Imaging is on
>>> by default for this command when box coordinates are present unless
>>> the 'noimage' keyword is specified.
>>>
>>> Hope this helps,
>>>
>>> -Dan
>>>
>>> PS - You can also find the maximum distance with the 'maxdist' keyword.
>>>
>>> On Mon, Jun 2, 2014 at 8:46 AM, newamber list <newamberlist.gmail.com>
>>> wrote:
>>> > Hi All
>>> >
>>> > This is an old mail regarding minimum distance between the images:
>>> >
>>> > http://archive.ambermd.org/200501/0024.html
>>> >
>>> > I am just wondering is it implemented now? I need to know the minimum
>>> > distance between the images and I can script down to calculate for each
>>> > pair of atoms but would be good to know if any inbuilt command can help
>>> in
>>> > that?
>>> >
>>> > thanks in advance
>>> > JIom
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe, PhD
>>> Department of Medicinal Chemistry
>>> University of Utah
>>> 30 South 2000 East, Room 201
>>> Salt Lake City, UT 84112-5820
>>> http://home.chpc.utah.edu/~cheatham/
>>> (801) 587-9652
>>> (801) 585-6208 (Fax)
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jun 04 2014 - 11:30:02 PDT
