From: zeynab hoseyni (
Date: Mon Jun 14 2021 - 00:38:35 CDT

Dear Peter,

Thank you for your guidance. As you said, it seems the periodic cell height
does not match the carbon nanotube height. I checked the simulations
procedure and I discovered that during the initial preparation for the
simulation I performed a short NPT to get the uniform water density and
that's why the periodic cell height shrinked a bit while the CNT is
constrained to be fixed. I wonder if you can guide me how I can solve this
problem as the NPT simulation is needed.

All the Best,

*Zeynab *

On Sun, Jun 13, 2021 at 8:22 PM Peter Freddolino <> wrote:

> 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.
> Best,
> Peter
> 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 *