From: Peter Freddolino (
Date: Sun Jun 13 2021 - 19:22:32 CDT

Dear Zeynab,
It would be much easier to interpret your images if you provided the before
and after snapshots from the same perspective, and with the same graphical
representations. But just from what can be seen, are you sure that your
periodic cell height matches that of the nanotube? It looks like the water
doesn't extend that far up/down.

On Sun, Jun 13, 2021 at 4:50 PM zeynab hoseyni <> wrote:

> 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 *