[gmx-users] Regarding high RMSD

[Justin Lemkul]

On 1/17/20 11:01 PM, Ashma Khan wrote:
> Thank for your suggestion Alessandra
> I have applied the pbc conditions on my system in steps as follows:
> 1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc
> 2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o
> full_md_nojump.xtc
> 3. gmx trjconv -f full_md_nojump.xtc -s full_md.tpr -pbc mol -ur compact
> -center -o full_md_mol.xtc
> After applying all these conditions, peptides of dimer diffusing out of the
> box, both in opposite direction at the end of the simulation. kindly
> suggest me what should I do.
>

Center on one peptide only, to see if the other is re-wrapped in the 
central image along with it. If not, then you do not have a dimer at all 
times and the RMSD should be high. If they stay associated, re-calculate 
RMSD because the previous results were just a PBC artifact in that case. 
With any multimeric system, you cannot just center on "Protein" because 
the geometric center of the group can be exactly coincident with the 
center of the box with all the proteins at different faces/corners of 
the unit cell.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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