From: zeynab hoseyni (
Date: Sun Jun 13 2021 - 14:49:48 CDT

Hi All,

I'm simulating the bio-molecule (bmol) adsorption on carbon nano-tube (CNT)
solvated in a water box. The CNT is fixed along the z-axis during the
simulation and the height of the water box is the same as the height of the
CNT, in order to avoid entering water molecules into the CNT. Everything is
OK during the simulation (including minimization, equilibration and the NVT
simulation for the data collection). Since sometimes during the simulation
bmol leaves the primary water box (periodic boundary condition is applied),
it is needed to wrap bmol into the primary water box. I used to run the
following commands to wrap bmol into the cell with no problem:

package require pbctools
set nfiles 40
  set str ./reduced.psf
  mol new $str type psf waitfor all
  for {set j 4} {$j <= $nfiles} {incr j 4} {
  animate read dcd cnt-asp_red_$j.dcd waitfor all
  pbc wrap -centersel "resname CNT" -center com -compound residue -all
  set sel [atomselect top "all"]
  animate write dcd cnt-asp_red_wrap_$j.dcd sel $sel waitfor all
  animate delete all

But with this new setup (to consider the same height for the CNT and
simulation box) I see that after wraping the bmol into the cell, some extra
bonds appear on the top and bottom of CNT as it is seen in snapshots
uploaded in the following links:;!!DZ3fjg!rlsDeyMoYSCuNDiUiNpeuNjJetxTDMGt_NSLTbLQ7vkX7rzi8h5xs9dPJehhpsIMbg$;!!DZ3fjg!rlsDeyMoYSCuNDiUiNpeuNjJetxTDMGt_NSLTbLQ7vkX7rzi8h5xs9dPJegGgvi12A$;!!DZ3fjg!rlsDeyMoYSCuNDiUiNpeuNjJetxTDMGt_NSLTbLQ7vkX7rzi8h5xs9dPJejHWtCaJQ$

I followed several ways to get rid of those bonds but still unsuccessful.
Would be thankful if anyone guides me.

All the Best,

*Zeynab *