[AMBER] How to change the coordinates of the system

From: Maria Bzówka <m.bzowka.tunnelinggroup.pl>
Date: Mon, 15 Jul 2019 13:32:32 +0200

Hi all,

I work with the system which consists of 128 lipids bilayer and water
molecules. I used the cpptraj to center the whole system using following

trajin step6.1_equilibration.nc
trajin step6.2_equilibration.nc
trajin step6.3_equilibration.nc
trajin step6.4_equilibration.nc
trajin step6.5_equilibration.nc
trajin step6.6_equilibration.nc
autoimage origin
center :1-128 mass origin
image origin center familiar

In VMD the system itself looks fine, but when I wanted to check the pbc
box, it only partially overlaps with the system (you can see in the
attached file).
Should I somehow change the cpptraj commands?

Thank you in advance for suggestions


AMBER mailing list

(image/png attachment: vmd.png)

Received on Mon Jul 15 2019 - 05:00:03 PDT
Custom Search