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<P>Dear David,</P>
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<P>Maybe I did not express my question clearly. I use the same em.mdp(list below) and the same gro file but with the different content of posre.itp(first time: whole protein; second time: the mainchain of the protein; last time:only the Calpha of the protein). The rmsd ( last step structure to crystal structure) of every time is identical. So I think although I use "define = -DPOSRE" in em.mdp, the posre.itp is not be used in optimizing progress, otherwise I should get the different rmsd of every time. I guess that there is no position restraints in optimizing process whether using define = -DPOSRE or not.</P>
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<P>cpp = /lib/cpp<BR>define = -DPOSRE -DFLEX_SPC<BR>constraints = none<BR>integrator = steep<BR>nsteps = 100<BR>;<BR>; Energy minimizing stuff<BR>;<BR>emtol = 500<BR>emstep = 0.01</P>
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<P>nstcomm = 1<BR>ns_type = grid<BR>coulombtype = PME<BR>rlist = 0.9<BR>rcoulomb = 0.9<BR>rvdw = 0.9<BR>fourierspacing = 0.12<BR>pme_order = 4<BR>optimize_fft = yes<BR>Tcoupl = no<BR>Pcoupl = no<BR>gen_vel = no</P>
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<P> </P>
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<P>Xu yechun<BR><BR><BR></P>
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