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Hi,<br><br>This is something we forgot to update.<br>I fixed it for the next beta release.<br>If you can read/use diff's, you can fix it yourself with the diff below.<br><br>Berk<br><br>--- a/src/tools/gmx_membed.c<br>+++ b/src/tools/gmx_membed.c<br>@@ -3121,9 +3121,12 @@ double do_md_membed(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],<br> update_pcouple(fplog,step,ir,state,pcoupl_mu,M,wcycle,<br> upd,bInitStep);<br> <br>- /* velocity (for VV) */<br>- update_coords(fplog,step,ir,mdatoms,state,f,fr->bTwinRange && bNStList,fr->f_twin,fcd,<br>- ekind,M,wcycle,upd,FALSE,etrtVELOCITY2,cr,nrnb,constr,&top->idef);<br>+ if (bVV)<br>+ {<br>+ /* velocity half-step update */<br>+ update_coords(fplog,step,ir,mdatoms,state,f,fr->bTwinRange && bNStList,fr->f_twin,fcd,<br>+ ekind,M,wcycle,upd,FALSE,etrtVELOCITY2,cr,nrnb,constr,&top->idef);<br>+ }<br> <br> /* Above, initialize just copies ekinh into ekin,<br> * it doesn't copy position (for VV),<br><br><br><hr id="stopSpelling">Date: Tue, 24 Aug 2010 16:41:35 +0800<br>From: zhongjin1000@yahoo.com.cn<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Software inconsistency error: update_coords called for velocity without VV integrator<br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font: inherit;" valign="top"><div id="ecxyiv1295209572">
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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></tbody></table><br>
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