What happens if you just 'autoimage' (don't unwrap first)?
-Dan
On Thu, Jun 22, 2017 at 9:51 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in> wrote:
> Dear Fellows,
>
> I have performed a MD simulation with coordinates wrapping enabled. Now I
> am facing discontinuous trajectory problem. I tried to unwrap coordinates
> and reimage but it did not helped. Investigating about the cause of problem
> I found following things.
>
> 1. PBC Box dimensions: {88.588371 75.344688 67.300514 90.000000 90.000000
> 90.000000}
> 2. Protein dimension (distance between coordinates of extreme points in
> protein) as
> {63.625731468200684 49.82566452026367 40.63145446777344}
>
> Unwrapping and Imaging was done as below with cpptraj.
>
> parm com.wat.leap.prmtop
> trajin rst2_out.dcd 1 51000 10
> reference ../../../../02.leap/com/com.wat.leap.inpcrd
> unwrap byres reference !:1-287
> center :123.HE2 mass origin reference
> image origin center familiar com :123.HE2 byres !:1-287
> unwrap byatom reference :1-287
> center :123.HE2 mass origin reference
> image origin center familiar com :123.HE2 byatom :1-287
> trajout com.strip_cr14.nc
> go
>
> Atom :123.HE2 was nearest protein atom to the center of PBC box in initial
> coordinates, hence it was chosen for centering protein to the box.
>
> Now, problem is that molecule has rotated during the simulation in the box
> and hence atoms are crossing two opposite sides of the box at the same
> time. So, when it is wrapped these atoms are appearing from opposite of
> actual side it should be, leading to stretches of structure connected by
> bonds length of box-dimension.
>
> So, I tried to construct a cubic box of side length 20 with is center at
> the center of PBC-box.
> as follows.
>
> Let centre of PBC-box has coordinates {cx cy cz}
> then six-set of residues corresponding to residues beyond inner-cubic-box
> faces were selected as
>
> set rset1 [atomselect top "protein and x < cx - 10"]
> set rset1 [atomselect top "protein and x > cx + 10"]
> set rset1 [atomselect top "protein and y < cy - 10"]
> set rset1 [atomselect top "protein and y > cy + 10"]
> set rset1 [atomselect top "protein and z < cz - 10"]
> set rset1 [atomselect top "protein and z > cz + 10"]
>
> Now residues in these sets were unwraped
> centering was done with atom closet to the center of corresponding face of
> inner-cubic-box
> and image was done for these set of residues. but it dis not work
>
> Other suggested options were also tried e.g.
>
> unwrap
> autoimage
>
> with bymol, byres and byatom options with solute mask, all system mask, but
> yet to succeed.
>
> Any help and suggestions in regard will be greatly appreciated.
>
> Thank you.
>
> Image of system with/without box waters shown is attached. If required, I
> can share, prmtop and dcd files with some frames.
>
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>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Jun 22 2017 - 09:00:02 PDT
