Hi Acoot, Read the tutorial. It's explained there... Mind that that tutorial was written for an earlier version of Gromacs and some things have changed. The names of ions, for instance.
Cheers, Tsjerk On Mar 19, 2012 6:40 AM, "Acoot Brett" <[email protected]> wrote: Dear All, The problem really occurs in the ion addition step. 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. >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. For the top file, we modify it in the following way, 48 SOLs were deleted, 20 Na+ were added, and 28 Cl- added. 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)". Thus how do we modify the .gro file and the .top file so that the number of coordinated will be equal between them? Cheers, Acoot *From:* Justin A. Lemkul <[email protected]> *To:* Acoot Brett <[email protected]>; Discussion list for GROMACS users <[email protected]> *Sent:* Monday, 19 March 2012 12:06 PM *Subject:* Re: [gmx-users] number of coordinates in coordinate file does not match topology Acoot Brett wrote: > Dear All, > I am practicing the on-line tutorial http://www.nmr.chem.uu.nl... -- 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
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