Dear All,
I would like to calculate and compare the mean square displacement of
phopshate groups from POPC lipids vs time (using stfcdiffusion command from
cpptraj) for two systems.
In cpptraj I used the following commands to obtain the MSD vs time:
trajin x.nc
stfcdiffusion mask :POPC.P out MSD_POPC.dat xy
go
My .nc file was prepared in a way that I used the following cpptraj
commands:
trajin x1.nc
trajin x2.nc
...
autoimage
center ':POPC'
image :WAT,SOD,CLA
trajout x.nc
go
My question is if it's correct to use this commands or if I should use only
the "raw" trajectory from the simulation without any autoimage, center and
image options?
Thank you in advance
Maria
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Received on Wed Aug 21 2019 - 07:00:02 PDT
