Dear all,
I am using CPPTRAJ to calculate diffusion and mask. I found the results were different if I added "autoimage" in the script. I did not set iwrap in my MD input file. If I used VMD to check the trajectory file, I got an almost spherical water box. If I "autoimage" the trajectory file, I got a cubic waterbox. Which way is right for the calculation? I am really confused about how CPPTRAJ calculated for a PBC water box.
Thanks,
Xiaoquan.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 02 2015 - 13:30:03 PDT
