Dear Rick,

Thanks a lot for you kind answers.

As you mentioned, I tried all of them.

Here is my edited script (I modified a trajectory by setting the z values to 0):

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! Define correlation function

correl maxt 40000 maxs 1024 maxa 40000 noupdate

! Define timeseries

set n 1

set nresid 128

label enterloop

enter M@n atom xyz sele mass segid MEMB .and. resid @n end

incr n by 1

if @n .le. @nresid goto enterloop

! Read trajectories

open unit 10 file name 1ns_2d.dcd

traj first 10 nunit 1 nocheck

! Write timeseries

set n 1

set nseries 128

label writeloop

corfun M@n M@n diff

enter r@n dupl corr

edit r@n veccod 1 delta 0.002 skip 1 offset 1

open unit 10@n write card name msd_@n.dat

write r@n unit 10@n dumb time

* dummy

*

increase n by 1

if @n .le. @nseries goto writeloop

stop

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However, unfortunateIy, I could not see the exact accordance of time step.

As before, the data start from 1.000000 and the data end to 1.2540000.

Total number of data are 128 (from the output data) and there are 500 trajectories in a 1 dcd file (my trajectory file).

From the previous issue (

http://www.charmm.org/ubbthreads/ubbthre...=true#Post34584), I calculated lateral MSD using the coor analy command. It's input is:

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open read unit 101 file name 1ns_2d.dcd

traj query unit 101

traj iread 101 nread 1 skip 1000

calc nfile = ?NFILE

traj read

open unit 90 write form name 1ns_2d.msd

coor anal sele segid MEMB .and. resn DOPC end -

firstu 101 nunit 1 skip 1 -

imsd 90 ncors @nfile -

rspin 0.0 rspout 999.9 -

xbox @FFTX ybox @FFTY zbox @FFTZ

stop

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From the coor anal, I got the exact data that show exact time step matching.

However, I am not sure that the MSD and D values are exact things which are showed by a output file (I doubt whether diffusion coefficient is right or not) . So I want to check it by using the corral command.

I am looking forward your answers.

Thanks a lot.