dear Sir,
Thanks a lot for your reply.I am sorry for the fact that my subject name
does not tally with the problem I faced.I really apologize for that.
So I do not need to include explicitely "pbc=xyz" in my .mdp file as it
is already being used by default.
Regarding dssp I used the following commands
export DSSP=/home/debjani/dssp
setenv DSSP /home/debjani/dssp
do_dssp -s md.tpr -f traj.xtc
At the end of the program only the files namely ddEZ117f ddOWnvlx etc were
present, but no .xpm files were there.I want to get the plot of changing of
secondary structural elements during the run.PLease help.
regards
Sangeeta
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