I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm might provide good results.
But now I have some problems with minimization of my initial structure Firstly, I've performed steep minimization ( emtool=1000, emstep = 0.01 ) and than CG minimization (emtool=1, emstep = 0.001) but as the result I've obtain that my struucture didnt minimize properly. Is there any different strategies for the minimization for the ANM ? In addition I'd like to know about conditions of such normal mode simulations. Does this procedure require in the PBC ? ( I've performed all steps including energy minimization in vacuu) James 2011/10/25 Mark Abraham <mark.abra...@anu.edu.au> > On 25/10/2011 3:30 AM, James Starlight wrote: > > I understand this but I've not been able found such information. I dont > need in the most accurately parametries for all cutt-offs of my system but > I want to gain inside into the basic cutt- offs worked with the Normal mode > analysis. > > > The cut-offs are particular to the force field, not the manner in which the > force field is used (EM vs MD vs whatever). There are literature references > in the GROMACS manual, and also in the published work that you have been > reading because it has objectives similar to yours. (hint, hint) > > > E.g I've found that PME is not worked here. > > > PME does work here. Last time you were apparently mis-matching files... > > > So I must to constrain my system with simplest cuttoffs. Could you provide > me with the simple example e.g cutt of for interaction beetwen C-alpha atoms > only etc? > > > You can't do that, and shouldn't even if you could. > > Mark > > > > James > > > >> These are particular to the force field involved, not the software. >> Please consult the appropriate literature, and see what others have used for >> similar work. >> >> > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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