<div>Hi </div> <div> </div> <div>Thank you for your advices.I want to ask a question.Is there a difference in the MD simulation between A protein complex which has 2 chains and a molecule that has 1 chain?Are the parameters must be different ?Also I want to ask about trajconv.Where I had to add the pbc?I want to send you my directions.</div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt; mso-list: l0 level1 lfo1; tab-stops: list 18.0pt"><FONT face="Times New Roman"><SPAN style="COLOR: fuchsia; mso-fareast-font-family: 'Times New Roman'"><SPAN style="mso-list: Ignore"><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 style="mso-spacerun: yes"> </SPAN>1ppbfree.gro<SPAN style="mso-spacerun: yes"> </SPAN></FONT><?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="mso-spacerun: yes"><SPAN style="FONT-SIZE: 12pt; COLOR: fuchsia; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'MS Mincho'; mso-fareast-language: JA; mso-ansi-language: TR; mso-bidi-language: AR-SA">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; mso-list: l0 level1 lfo1; tab-stops: list 18.0pt"><FONT face="Times New Roman"><SPAN style="COLOR: fuchsia; mso-fareast-font-family: 'Times New Roman'"><SPAN style="mso-list: Ignore"><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><o:p> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt; mso-list: l0 level1 lfo1; tab-stops: list 18.0pt"><SPAN style="COLOR: fuchsia; mso-fareast-font-family: 'Times New Roman'"><SPAN style="mso-list: Ignore">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; mso-list: l0 level1 lfo1; tab-stops: list 18.0pt"><SPAN style="COLOR: fuchsia"><o:p><SPAN style="FONT-SIZE: 12pt; COLOR: fuchsia; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 'MS Mincho'; mso-fareast-language: JA; mso-ansi-language: TR; mso-bidi-language: AR-SA">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></o:p></SPAN></div></o:p></FONT></SPAN></FONT> <div> </div> <div>or is the pbc used in the script?</div> <div>Thank You very much....</div> <div>Özge</div> <div> </div><p> 
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