<div>Hi Eric,</div> <div> </div> <div>Where is the specbond.dat?After which line is it formed?</div> <div> </div> <DIV class=MsoNormal style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt"><FONT face="Times New Roman"><SPAN style="COLOR: fuchsia"><SPAN><FONT size=3>1.</FONT><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN style="COLOR: fuchsia"><FONT size=3>pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o<SPAN> </SPAN>1ppbfree.gro<SPAN> -merge</SPAN></FONT></SPAN></FONT></DIV> <DIV class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN><SPAN style="FONT-SIZE: 12pt; COLOR: fuchsia; FONT-FAMILY: 'Times New Roman'">2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron</SPAN></SPAN></DIV> <DIV class=MsoNormal style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt"><FONT face="Times New Roman"><SPAN style="COLOR: fuchsia"><SPAN><FONT size=3>3.</FONT><SPAN style="FONT: 7pt 'Times New
Roman'"> </SPAN></SPAN></SPAN><SPAN style="COLOR: fuchsia"><FONT size=3>genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro</FONT></SPAN></FONT></DIV><FONT face="Times New Roman"><SPAN style="COLOR: fuchsia"><FONT size=3> <DIV class=MsoNormal style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt"><SPAN style="COLOR: fuchsia"><SPAN>4.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN style="COLOR: fuchsia">grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top</SPAN></DIV> <DIV class=MsoNormal style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt"><SPAN style="COLOR: fuchsia"><SPAN style="FONT-SIZE: 12pt; COLOR: fuchsia; FONT-FAMILY: 'Times New Roman'">5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr</SPAN></SPAN></DIV></FONT></SPAN></FONT> <DIV>Please help me?:)</DIV> <DIV> </DIV>
<DIV>özge</DIV><p> 
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