I REALLY need some help here. I have tried for several days now and looked on
line to fix the situation. My protein moves around and goes outside the
simulation waterbox and my Zinc ions also frequently have bonds to protein of
40 angstroms are so.
Here is one of the combinations I have tried
Hi Steve,
Did you try a plain -fit rot+trans in trjconv. That should remove both com
translation as well as rotation. Select the 'protein' group for the least
squares fit.
On Tue, May 27, 2014 at 1:09 AM, Steve Seibold steve...@ymail.com wrote:
I REALLY need some help here. I have tried for
On 5/26/14, 3:39 PM, Steve Seibold wrote:
I REALLY need some help here. I have tried for several days now and looked on
line to fix the situation. My protein moves around and goes outside the
simulation waterbox and my Zinc ions also frequently have bonds to protein of
40 angstroms are so.
Hi
Just a suggestion:
Try first to concatenate all the trajectory with trjcat and then
remove the periodicity effects with trjconv with the flag -pbc nojump.
Best regards
Paulo Netz
2014-05-26 16:39 GMT-03:00 Steve Seibold steve...@ymail.com:
I REALLY need some help here. I have tried for
