Dear all,<br>My system is based on Martini, needs a dodehedron box. <br>Initially, it was minimized and equilibrated with a cubic box smoothly. Then I used the follow command to <br>translate the box in to dodehedron:<br> editconf -f f0.gro -bt dodecahedron -d 2 -o vesdode.gro <br>
But with this change, the simulation always blows up with the message below.<br><br>Since those atoms are most at the boundary of the box, I think it is because the overlap of boundary atoms <br>with the new box type. I tried different value for -d and -box, but still have the same problem.<br>
<br>Can anybody give me any hint to fix this? <br><br>Thanks a lot!<br>Zhenlong<br><br>---------------------------------------------------------------------------------------------------------------------------------<br>Making 3D domain decomposition 7 x 4 x 3<br>
<br>A list of missing interactions:<br> Bond of 79872 missing 7<br> G96Angle of 50688 missing 9<br><br>Molecule type 'DPPC'<br>the first 10 missing interactions, except for exclusions:<br>
G96Angle atoms 6 7 8 global 37638 37639 37640<br> Bond atoms 7 8 global 37639 37640<br> G96Angle atoms 10 11 12 global 37642 37643 37644<br> Bond atoms 11 12 global 37643 37644<br>
<br>Molecule type 'DUPC'<br>the first 10 missing interactions, except for exclusions:<br> G96Angle atoms 10 11 12 global 38446 38447 38448<br> Bond atoms 11 12 global 38447 38448<br>
<br>Molecule type 'DPPC'<br>the first 10 missing interactions, except for exclusions:<br> G96Angle atoms 3 5 6 global 43395 43397 43398<br> Bond atoms 5 6 global 43397 43398<br>
G96Angle atoms 5 6 7 global 43397 43398 43399<br><br>Molecule type 'DUPC'<br>the first 10 missing interactions, except for exclusions:<br> G96Angle atoms 6 7 8 global 45330 45331 45332<br>
Bond atoms 7 8 global 45331 45332<br><br>Molecule type 'DUPC'<br>the first 10 missing interactions, except for exclusions:<br> G96Angle atoms 5 6 7 global 57173 57174 57175<br>
Bond atoms 6 7 global 57174 57175<br> G96Angle atoms 6 7 8 global 57174 57175 57176<br><br>Molecule type 'DPPC'<br>the first 10 missing interactions, except for exclusions:<br>
G96Angle atoms 6 7 8 global 63822 63823 63824<br> Bond atoms 7 8 global 63823 63824<br><br>