Dear All, I have a simulation box of dimension 8*6*4 nm3. The center of the box is the center of the two center of masses of two ss-DNA. I want to calculate the 2D distribution of the ions surround the strands in the box. I chose Chain_A, Chain_B and ion as three groups, rather I am confused with the options that should be added to have the correct dimension of the finally produced image. what argument I should add for -amax and -rmax? Anything else I have to use in the command line? The colour is also not shown , what is the reason? can anyone please tell me Thanks in advance
On Mon, May 28, 2018 at 1:04 PM, Alex <nedoma...@gmail.com> wrote: > > That's not my intention - someone seeking a topology would do well to a) >> know the past research to inform their decisions, including whether to >> repeat deliberately, and b) also ask them to share input files. >> >> I was obviously joking, not to derail this thread. Besides, in > biomolecular fields, FF development in general and topology building in > particular, you guys have at least some unity in how to approach things. In > solid state (or solid-liquid systems), we have a pretty arbitrary zoo. The > cherry on top of this cake is recent OPLS-AA-based FF for two widely > studied nanomaterials with partial charges coming from DDAP, which is > entirely different from CHELPG used for OPLS originally. And everything > fits everything! > >> A lot of past work is horrible, yes :-) >> >> Always! > > Alex > > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- SOHAM SARKAR Junior Research Fellow Department of Chemistry INDIAN INSTITUTE OF TECHNOLOGY BOMBAY -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.