[gmx-users] solvent except water

Hi what command and what option apply solvent except water in MD simulation by gromacs. Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

Re: [gmx-users] solvent except water

leila karami wrote: Hi what command and what option apply solvent except water in MD simulation by gromacs. Any help will highly appreciated! WHat do you mean? -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University.

[gmx-users] solvent except water

Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

Re: [gmx-users] solvent except water

leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue

Re: [gmx-users] solvent except water

Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: leila karami wrote:

Re: [gmx-users] solvent except water

rasoul nasiri wrote: Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? You can use genbox with mixed solvents. I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM,

Re: [gmx-users] solvent except water

David van der Spoel wrote: rasoul nasiri wrote: Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? You can use genbox with mixed solvents. There are even how-to's on the Gromacs site to accomplish this: