VMD-L Mailing List

From: Amnah Alalmaie (aalalmaie_at_mail.usciences.edu)
Date: Thu Mar 18 2021 - 15:43:30 CDT

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