Ok I sent it. Let me know if you did not receive them. Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering [email protected]
On Dec 31, 2012, at 5:54 PM, Justin Lemkul <[email protected]> wrote: > > > On 12/31/12 5:50 PM, Xu Dong Huang wrote: >> Dear Justin, >> >> I'm pretty sure my .gro file is valid, here is a direct copy and paste of >> the format of my .gro in the beginning: >> >> star polymer >> 201 >> 1star O4 1 0.000 0.000 0.000 >> 1star O1 2 0.430 0.000 0.000 >> 1star O1 3 0.860 0.000 0.000 >> 1star O1 4 1.290 0.000 0.000 >> 1star O1 5 1.720 0.000 0.000 >> 1star O1 6 2.150 0.000 0.000 >> 1star O1 7 2.580 0.000 0.000 >> 1star O1 8 3.010 0.000 0.000 >> 1star O1 9 3.440 0.000 0.000 >> 1star O1 10 3.870 0.000 0.000 >> 1star O1 11 4.300 0.000 0.000 >> 1star O1 12 4.730 0.000 0.000 >> 1star O1 13 5.160 0.000 0.000 >> 1star O1 14 5.590 0.000 0.000 >> 1star O1 15 6.020 0.000 0.000 >> 1star O1 16 6.450 0.000 0.000 >> 1star O1 17 6.880 0.000 0.000 >> 1star O1 18 7.310 0.000 0.000 >> 1star O1 19 7.740 0.000 0.000 >> 1star O1 20 8.170 0.000 0.000 >> ... >> >> and for the output .gro after editconf, here is what it shows (I don't know >> why the formats are kind of shifted, ) >> >> star polymer >> 201 >> 1star O4 1 11.921 11.921 16.195 >> 1star O1 2 12.351 11.921 16.195 >> 1star O1 3 12.781 11.921 16.195 >> 1star O1 4 13.211 11.921 16.195 >> 1star O1 5 13.641 11.921 16.195 >> 1star O1 6 14.071 11.921 16.195 >> 1star O1 7 14.501 11.921 16.195 >> 1star O1 8 14.931 11.921 16.195 >> 1star O1 9 15.361 11.921 16.195 >> 1star O1 10 15.791 11.921 16.195 >> 1star O1 11 16.221 11.921 16.195 >> 1star O1 12 16.651 11.921 16.195 >> 1star O1 13 17.081 11.921 16.195 >> 1star O1 14 17.511 11.921 16.195 >> 1star O1 15 17.941 11.921 16.195 >> ... >> >> Another reason why I think my .gro is valid is that when I editconf, it >> says: Read 201 atoms …blah blah blah.. , as it should I'm assuming if the >> .gro is valid? >> >> Please let me know, thank you. >> > > Yes, those files should be fine. Can you send me the two coordinate files > (off-list) so I can investigate what's going on? > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
