[gmx-users] g_dist lifetime option

Dear gromacs users,I have a comprehension question to g_dist with the lifetime(-lt) option.I want to determine the lifetime of a certain sidechain - ion contact (I use all ions as a group) within a radis of 0.6 nm.output:@    title "a_538 - K within 0.6 nm"@    xaxis  label "Time (ps)"@    yaxis  l

[gmx-users] LJ parameter : geometric / arithmetic average

Dear all,Could somebody tell me please, where I can switch from geometric to arithmetic average (for LJ parameter) ?Page 62 of the 4.5.4 manual.What's taken as default ?Thanks a lot.Mark  SMS schreiben mit WEB.DE FreeMail - einfach, schnell und   kostenguenstig. Jetzt gleich testen! http://f.web.de

[gmx-users] dihedral restraint violation output

Dear Gromacs users,I would like to ask how I could vizualise the violations of the dihedral restraints in detail, i.e., a list of all violations.As far as I know, there is nothing like g_disre for dihedrals, or ?Kind regardsMarkus  SMS schreiben mit WEB.DE FreeMail - einfach, schnell und   kostengu

Re: [gmx-users] protein-water distance restraints

treff: Re: [gmx-users] protein-water distance restraintsDear Markus,If you know the residues composing the cavity (and I think you know it), you can simply change the coordinatesof the water molecule in the .gro file to move the water in the cavity.FrancescoIl 12/10/2011 18:17, Markus Weingarth

[gmx-users] protein-water distance restraints

Dear Gromacs-users,I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation.I though that I could implement intermolecular distance restraints between a water r