<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear All,</span></div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div id="yiv311233958"><div><div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><div><span></span> </div><div><span>The problem really occurs in the ion addition step.</span></div><div><span></span> </div><div><span>In order to keep 0.1 M ion concentration, 20 Na+ and 20 C1- were added. In order to keep 0 charge, 8 Cl- were added.</span></div><div><span></span> </div><div><span>From the .gro file, 48 water (72 H and 48 O) were deleted in order to add the 38 charges, which makes there was a 96 atom
reduction.</span></div><div><span></span> </div><div><span>For the top file, we modify it in the following way, 48 SOLs were deleted, 20 Na+ were added, and 28 Cl- added.</span></div><div><span></span> </div><div><span>In the above manner, however, it indicated the " number of coordinates in coordinate file (1LW9-EM-solvated.gro, 32748) does not match
topology (1LW9.top)".</span></div><div><span></span> </div><div><span>Thus how do we modify the .gro file and the .top file so that the number of coordinated will be equal between them?</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot<var id="yiv311233958yui-ie-cursor"></var></span></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="yiv311233958hr"></div> <b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Acoot Brett <acootbrett@yahoo.com>; Discussion list
for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Monday, 19 March 2012 12:06 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] number of coordinates in coordinate file does not match topology <br> </font> </div> <br><br><br>Acoot Brett wrote:<br>> Dear All,<br>> I am practicing the on-line tutorial <a href="http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/" rel="nofollow" target="_blank">http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/</a>.<br>> In the step "mdrun -v -deffnm 1LW9-EM-solvated" of "Energy minimization of the solvated system", it says "<br>> Converged to machine precision , but not to the requested precision Fmax < 1". Before this step, all the other steps run fine.<br>> In the step "grompp -v -f pr.mdp -c 1LW9-EM-solvated.gro -p 1LW9.top -o 1LW9-PR.tpr" of "Relaxation of solvent and hydrogen
atom positions:
Position restrained MD", it says "<br>> Fatal error: number of coordinates in coordinate file (1LW9-EM-solvated.gro, 32748) does not match topology (1LW9.top, 0)"<br>> I am looking forward to getting a reply from you on how to what leads to the error message.<br>> <br><br><a href="http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology" rel="nofollow" target="_blank">http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology</a><br><br>You need to make sure the contents of the [molecules] directive always matches that of the coordinate file, in terms of the number of molecules and the order in which they are present.<br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia
Tech<br>Blacksburg,
VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" rel="nofollow" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br> </div> </div> </div></div></div><meta content="on" http-equiv="x-dns-prefetch-control"><br><br> </div> </div> </div></body></html>