Dear Amber users,
I am having some trouble in the correction of COM drift in my lipid system so I can calculate diffusion coefficients.
I have found the movement of the upper monolayer COM using the cpptraj commands:
trajin bilayer_run.nc
vector com center out upper_movement.dat :1-192
run
I have created the new prmtop and trajectory of the upper monolayer only:
parm DOPC.prmtop
trajin DOPC.nc
strip !(:1-192) outprefix upper
trajout DOPCupper.nc
run
I am unsure about how to reset the monolayer by the corresponding movement (in X, Y, Z) to create a new trajectory without monolayer COM drift.
Any help is appreciated,
Christopher Faulkner
PhD student
Cardiff University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 22 2018 - 02:00:02 PDT
