From: Ashar Malik (
Date: Thu Mar 18 2021 - 18:02:35 CDT


There is no way around this.
Because of the shape of your system and your desire for explicit solvation
you will have to work with a large number of atoms.

If you want to reduce the atoms of your system the alternate is to
compromise on quality and go with an implicit solvent simulation.


On Fri, Mar 19, 2021 at 4:58 AM Amnah Alalmaie <>

> Dear VMD users
> I am trying to simulate a system that has (protein + dsDNA) But the
> problem is with the solvation box. There is a dsDNA segment showing outside
> the box
> I used a triclinic box shape and center the complex in the box with 1.5 nm
> from the box edge, I have tried to increase the box size and use different
> box shape, but the number of atoms was very high (IM atoms )
> I used GROMACS
> I would like to hear your recommendations to solve this problem
> I really appreciate your help
> Thank you very much
> Amnah