Hi,
If you're using the 'stfcdiffusion' command you should 'unwrap' your
trajectory prior to the command since 'stfcdiffusion' does not correct
for imaging (like 'diffusion' does), e.g.:
unwrap
stfcdiffusion ...
Bottom line is that if you use any commands that artificially
translate your coordinates (like imaging commands) you will affect the
results of 'stfcdiffusion'.
-Dan
On Wed, Aug 21, 2019 at 9:38 AM Maria Bzówka <m.bzowka.tunnelinggroup.pl> wrote:
>
> 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 Tue Sep 03 2019 - 11:00:02 PDT
