Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? If you want to place several identical solutes with genbox -ci, then you could copy the file vdwradii.dat

[gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Thanks for helping! Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Position your solutes using editconf -center, then add solvent. -Justin Thanks for helping! Rasoul

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? Rasoul On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear All, Hello I understand

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Justin A. Lemkul wrote: rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is distributed in the

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

rasoul nasiri wrote: Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

Thanks for the information. Because of haven't satisfactory model from my co-solvent and I have to add it randomly along with the solvent by genbox -ci -nmol. the reason of this criteria relate to crash of system (solute+co-solvent+solvent) in the first step of simulation, because small distance