<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%"><SPAN style="COLOR: black">Dear users,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></div>
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<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black">I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K. after 1ns of simulation in 300 K, the protein jumps out of the box and when I use the command<o:p></o:p></SPAN></div>
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<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black"> trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump <o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black"> <o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black">followed by <o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black"> <o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black"> trjconv_mpi -f new*.trr -s *.tpr -o new*.pdb -dump 1000 <o:p></o:p></SPAN></div>
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<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black">the box shape changes from dodecahedron to spherical. In Gromacs manual I read ; <o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%"><SPAN style="COLOR: black"><o:p> </o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black">" There are several possible shapes for space-filling unit cells. Some, as the <I style="RIGHT: auto">rhombic dodecahedron </I>and the <I style="RIGHT: auto">truncated octahedron </I> approach a spherical shape better than a cubic box and are therefore more economical for studying an (approximately spherical) macromolecule in solution, since less solvent molecules are required to fill the box given a minimum distance between macromolecular images....... ". <o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%"><SPAN style="COLOR: black"><o:p> </o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black">Does it mean that it is ok and I can continue the simulation or I have to increase the box size? After simulation in 200 K the protein juped out of the box but using the same command the problem was fixed, without changing the box shape.<o:p></o:p></SPAN></div>
<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black">Thank you in advance for the help<o:p></o:p></SPAN></div>
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<div style="TEXT-ALIGN: justify; LINE-HEIGHT: 150%; RIGHT: auto"><SPAN style="COLOR: black">Sogol<o:p></o:p></SPAN></div>
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