VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Tue Nov 05 2019 - 10:25:13 CST

Dear VMD users,

I am having trouble with the RMSF calculations. I am using a script to
calculate RMSF.

System: Protein solvated in water with Ligands surrounding it.

As my simulation progresses, some chains of the protein came out of the box
and due to PBC, it entered from the other side. To fix this issue I
Unwrapped and wrapped the trajectory. The following commands were performed:

1) pbc unwrap -all -sel "not water" %% To save time I did not unwrap
water.
2) pbc wrap -all -compound fragment -center com -centersel protein

I am getting huge differences in RMSF in Raw (without wrapping) trajectory
and with wrapping trajectory. Which one should I consider? However, RMSD
in both cases is the same. Is the alignment of chains is different after
wrapping?

RMSF script:
Before sourcing the below script alignment is done through RMSD trajectory
tool "Align" option
##Alignment of alpha carbons with the reference frame##
proc rmsf_ca {seltext1 seltext2} {
set ca [atomselect top "$seltext1 and name CA"]
set rmsf [measure rmsf $ca]
set outfile [open "${seltext2}.dat" w]
set count 1
foreach x $rmsf {
puts "rmsf of $count is $x"
#set k [expr $x/10]
puts $outfile "$count $x"
incr count
}
puts "done"
close $outfile
}

Thank You.