Re: [gmx-users] steady

shahrbanoo karbalaee wrote: thank you justin . would you please tell me how can it equilbrated?is it the table rmsd aor visualization?or the time pr-md for 10 ns is enough (for tfe and spce)? Such information is usually based on experimental observables (density, heat capacity, etc.) I

RE: [gmx-users] steady

> Date: Thu, 9 Oct 2008 08:44:15 -0400 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] steady > > > > shahrbanoo karbalaee wrote: > > Dear justin > > > > a) if I want to have the steady and hemogen for mix so

Re: [gmx-users] steady

shahrbanoo karbalaee wrote: Dear justin a) if I want to have the steady and hemogen for mix solvent , do I have to use this command (when I made genbox box 16.16.24 before that)? :editconf -f conf.gro -bt dodecahedron -d 0.5 -o box.gro This will not homogenize anything; it only sets up

Re: [gmx-users] steady

shahrbanoo karbalaee wrote: Dear justin I made a file with (n1/n2=30) two solvents.I want to equilbrate this file.then I must minimize and run md(pre md ).please correct me if It is not right. I use editconf -f test42.pdb(this file)-bt dodecahedron - d 0.5 -o box.gro as you tell for

Re: [gmx-users] steady

shahrbanoo karbalaee wrote: Dear justin you are right .that file was distorted.I used -pbc without no jump.I need to use trjconv for minimized the box .please advise me. What file? What does it mean "without nojump"? Why do you need to use trjconv? If you're running MD, the first step i

Re: [gmx-users] steady

shahrbanoo karbalaee wrote: hi justin in during making mix solvent (30% for example) after making box I use trjconv -pbc .My pdb file lost the the arrange and it need long time for equilbrate and steady density.Is it right? or any suggestion about it? What option are you giving trjconv -