Dear Dan;
Thanks so much for your reply.
But, I am still confused about the 'image' in hbond.
I cannot understand what you said: "It doesn't matter if you first image the trajectory prior to 'hbond' if afterwards the hydrogen bond still exists across a periodic boundary."
If image the trajectory first , receptor and ligand should all be moved to the origin or center of box, so, there exists no molecules across periodic boundary after imaging. Does this MATTERs the hbond calculate?
What I want to express is that: when ligand just across a periodic boundary in one frame, and receptor still live in original unit cell,in such case, if no any image action used, hbond cannot be calculated correctly. But if using 'autoimage' after loading frames, I think it should be ok, like RMS, the molecules go to neighbor box will be back to former. Distance and angles should correctly calculated. (If I understand right)
So, I am still puzzled about the two 'image' actions, for why they give diffferent results.
Best,
Chris
At 2016-01-08 01:50:45, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>On Wed, Jan 6, 2016 at 8:46 PM, Chris <dlutlife223.163.com> wrote:
>> The result is markedly different only because of the image.
>> so£¬what make me confused is the image. In my option, if trajectory need imaged, it is the same for using 'autoimage' in cpptraj and 'image' in hbond command. Can someone explain such problem.
>
>The only way to detect hydrogen bonds across periodic boundaries is to
>use the 'image' keyword with 'hbond'. Otherwise the distances and
>angles in the 'hbond' command are calculated without knowledge of the
>unit cell. It doesn't matter if you first image the trajectory prior
>to 'hbond' if afterwards the hydrogen bond still exists across a
>periodic boundary.
>
>Hope this helps,
>
>-Dan
>
>
>--
>-------------------------
>Daniel R. Roe, PhD
>Department of Medicinal Chemistry
>University of Utah
>30 South 2000 East, Room 307
>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 Thu Jan 07 2016 - 11:00:03 PST
