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<DIV>Hi ,</DIV>
<DIV> When I use g_membed in GMX4.5.3 Beta 3 to insert a protein into a DMPC bilayer, I came across such an error:</DIV>
<DIV>Program g_membed, VERSION 4.5-beta3<BR>Source code file: update.c, line: 1595</DIV>
<DIV>Software inconsistency error:<BR>update_coords called for velocity without VV integrator<BR>For more information and tips for troubleshooting, please check the GROMACS<BR></DIV>
<DIV> </DIV>
<DIV>g_membed -f gmem.tpr -p 1b8l.top -xyinit 0.5 -xyend 1 -nxy 1000 -ndiff 11 -c OK.pdb</DIV>
<DIV> </DIV>
<DIV>Reading file gmem.tpr, VERSION 4.5-beta3 (single precision)<BR>Reading file gmem.tpr, VERSION 4.5-beta3 (single precision)</DIV>
<DIV>Select a group to embed in the membrane:<BR>Group 0 ( System) has 16956 elements<BR>Group 1 ( Protein) has 3708 elements<BR>Group 2 ( Protein-H) has 2904 elements<BR>Group 3 ( C-alpha) has 388 elements<BR>Group 4 ( Backbone) has 1164 elements<BR>Group 5 ( MainChain) has 1556 elements<BR>Group 6 ( MainChain+Cb) has 1904 elements<BR>Group 7 ( MainChain+H) has 1940 elements<BR>Group 8 ( SideChain) has
1768 elements<BR>Group 9 ( SideChain-H) has 1348 elements<BR>Group 10 ( Prot-Masses) has 3708 elements<BR>Group 11 ( non-Protein) has 13248 elements<BR>Group 12 ( Other) has 13248 elements<BR>Group 13 ( DMPC) has 13248 elements<BR>Select a group: 1<BR>Selected 1: 'Protein'</DIV>
<DIV>Select a group to embed Protein into (e.g. the membrane):<BR>Group 0 ( System) has 16956 elements<BR>Group 1 ( Protein) has 3708 elements<BR>Group 2 ( Protein-H) has 2904 elements<BR>Group 3 ( C-alpha) has 388 elements<BR>Group 4 ( Backbone) has 1164 elements<BR>Group 5 ( MainChain) has 1556 elements<BR>Group 6 ( MainChain+Cb) has 1904 elements<BR>Group 7 ( MainChain+H) has 1940 elements<BR>Group 8 (
SideChain) has 1768 elements<BR>Group 9 ( SideChain-H) has 1348 elements<BR>Group 10 ( Prot-Masses) has 3708 elements<BR>Group 11 ( non-Protein) has 13248 elements<BR>Group 12 ( Other) has 13248 elements<BR>Group 13 ( DMPC) has 13248 elements<BR>Select a group: 13<BR>Selected 13: 'DMPC'<BR>The estimated area of the protein in the membrane is 15.930 nm^2</DIV>
<DIV>There are 130 lipids in the membrane part that overlaps the protein.<BR>The area per lipid is 0.6809 nm^2.<BR>Maximum number of lipids that will be removed is 46.</DIV>
<DIV>Will resize the protein by a factor of 0.500 in the xy plane and 1.000 in the z direction.<BR>This resizing will be done with respect to the geometrical center of all protein atoms<BR>that span the membrane region, i.e. z between 1.299 and 6.362</DIV>
<DIV>Embedding piece 0 with center of geometry: 4.933612 4.933665 3.830500</DIV>
<DIV>Will remove 0 Protein_chain_A molecules<BR>Will remove 0 Protein_chain_B molecules<BR>Will remove 0 Protein_chain_C molecules<BR>Will remove 0 Protein_chain_D molecules<BR>Will remove 37 DMPC molecules</DIV>
<DIV>Back Off! I just backed up 1b8l.top to ./#1b8l.top.2#</DIV>
<DIV>Back Off! I just backed up traj.trr to ./#traj.trr.1#</DIV>
<DIV>Back Off! I just backed up traj.xtc to ./#traj.xtc.1#</DIV>
<DIV>Back Off! I just backed up ener.edr to ./#ener.edr.1#<BR>starting mdrun 'God Rules Over Mankind, Animals, Cosmos and Such'<BR>1000 steps, 2.0 ps.</DIV>
<DIV>-------------------------------------------------------<BR>Program g_membed, VERSION 4.5-beta3<BR>Source code file: update.c, line: 1595</DIV>
<DIV>Software inconsistency error:<BR>update_coords called for velocity without VV integrator<BR>For more information and tips for troubleshooting, please check the GROMACS<BR>website at <A href="http://www.gromacs.org/Documentation/Errors" rel=nofollow target=_blank>http://www.gromacs.org/Documentation/Errors</A><BR>-------------------------------------------------------</DIV>
<DIV>"Look at these, my work-strong arms" (P.J. Harvey)</DIV>
<DIV> </DIV>
<DIV>How to solve such an problem? Thanks!</DIV>
<DIV> </DIV>
<DIV>Zhongjin He</DIV></TD></TR></TBODY></TABLE></DIV></td></tr></table><br>