<div>Hi everybody,</div> <div> </div> <div>I have a problem with my molcule.I have protein- ligand complex.One of my friends works with the same ligand.First of all we use the same mdp files.We made the simulation.But my calculations were halted.This is the error :</div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>Error on node 1, will try to stop all the nodes</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>Halting parallel program mdrun_mpi on CPU 1 out of 8</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3>7 additional processes aborted (not shown)</FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p><FONT face="Times New Roman" size=3> I only can think about the difference may be caused because of my protein -ligand complex is
very big.It has 2 chains.</FONT></o:p></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p></o:p> </div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt">After that I changed <FONT face="Times New Roman" size=3>nstcomm<SPAN style="mso-spacerun: yes"> ,</SPAN></FONT><FONT face="Times New Roman" size=3>nstxout<SPAN style="mso-spacerun: yes"> ,</SPAN></FONT><FONT face="Times New Roman" size=3>nstvout<SPAN style="mso-spacerun: yes"> ,</SPAN></FONT><FONT face="Times New Roman" size=3>nstfout,<SPAN style="mso-spacerun: yes"> </SPAN></FONT><FONT face="Times New Roman" size=3>nstlog<SPAN style="mso-spacerun: yes"> ,</SPAN></FONT><FONT face="Times New Roman" size=3>nstenergy,<SPAN style="mso-spacerun: yes"> </SPAN></FONT><FONT face="Times New Roman" size=3>nstxtcout<SPAN style="mso-spacerun: yes"> values than it started to run. But the graphics after the analyze part(rmsd,gyration...) are very bad.I saw
very sharp and meaningless pics.Then I would like to do the same thing with a paper.In this paper they made the calculation for 50 ps with position restarint.After they made for 50 ps without position restraint.At the end they made for 20 ns again full mdp.Idid the same.But the gyration and rmsd calculations are not the same.Again meaningless graphics.I have tried to solve the problems for two months.If anything exist to solve the problems I can send my mdp files.Is there a mistake for my mdp files?</SPAN></FONT></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3><SPAN style="mso-spacerun: yes"></SPAN></FONT> </div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size=3><SPAN style="mso-spacerun: yes">thank you ..</SPAN></FONT></div><p> 
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