please some one can help me on this problem. I need to get visualization of a peptide which was equilibrate in water box. The peptide was split to two parts and I need to connect it in to a one molecule. I need to fix this because to get correct RMSD graph of the structure. Thanks.
This is due to protein crossing the box boundaries. So I think the RMSD value VMD gives is correct.
If you want a nicer representation, you can try
1. shift the simulation box boundaries by using one of these,
i. pbc wrap -orthorhombic -shiftcenterrel {x y z}
ii. pbc box -center origin -shiftcenter {x y z}
iii. pbc wrap -center origin -compound fragment -shiftcenterrel "$x $y $z"
2. move the whole protein (which changes the coordinates)
set pdbCenter [measure center $sel weight mass]
set offset [vecsub {40. 40. 40.} $pdbCenter]
$sel moveby $offset
Cheers,
MR
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