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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 22 2017 - 07:00:03 PDT
