Hi I am trying to use g_membed to insert a protein into a bilayer. I made some changes to the sample.mdp file downloaded from the authors' homepage. The changes were:
- reduced time step to 0.001 ps (instead of 0.002) - changed constraints to hbonds instead of all-bonds. g_membed runs fine, but stops only after one iteration after which the protein is of course shrunk. The command used is: echo 20 16 | g_membed -f membed.tpr -n membed.ndx -xyinit 0.1 -xyend 1.0 -nxy 1000 -maxwarn 10 I am wondering what is going on ? Also, is there a way to parallelize g_membed? -- Maria G. Technical University of Denmark Copenhagen
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