----- Original Message ----- From: 张春雷 <[email protected]> Date: Friday, June 25, 2010 18:06 Subject: Re: [gmx-users] Optimizing system size by moving from rectangular to hexagonal cells To: Discussion list for GROMACS users <[email protected]>
> I think you may try "trjconv -ur". I don't think that can work, because the OP needs to remove a subset of molecules, and trjconv -ur can't do that. I am not aware of any GROMACS tool that might serve the purpose. I suspect the only reasonable solutions are to equilibrate the hexagonal cell from scratch, or to write a script to apply the new unit cell boundaries, and then re-equilibrate. Mark > 2010/6/25 Marc Baaden <[email protected]> > > Dear All, > > Trying to optimize some simulation systems, I noticed that I could > actually gain quite some degrees of freedom by changing the xy > dimension of my simulation system from square/rectangular to hexagonal. > I wonder how one would do that in order to preserve at best the > properties of an already equilibrated system with a rectangular > xy-plane. Can Gromacs simply "cut" a hexagonal patch out of a periodic > simulation box with rectangular geometry? > Which tool would one use for this task? Editconf, with options eg > -c -box a b c -angles 120 120 90 ? > > Thank you very much in advance, > Marc Baaden > > -- > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > mailto:[email protected] - http://www.baaden.ibpc.fr > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
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