VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Mar 18 2021 - 18:02:35 CDT

Hi,

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.

Best,
/A

On Fri, Mar 19, 2021 at 4:58 AM Amnah Alalmaie <aalalmaie_at_mail.usciences.edu>
wrote:

> 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
>