[gmx-users] Re: box volume and solvant density

Le lundi 31 mai 2010 à 10:29 -0400, Justin A. Lemkul a écrit : > > Justin A. Lemkul wrote: > > > > > > grivet wrote: > >> Dear all, > >> > >> I am running simulations of pure water at various temperatures. My first > >> step i

[gmx-users] box volume and solvant density

of water in the NVT run ? Using g_density, I am surprised to find that the density is varying by several percent; shouldn't it remain constant ? Thanks in advance for your insights JP Grivet -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] output in gromos format

xtc_precision; what does it mean? Another quite unrelated question; most examples I have looked at use rvdw = 1.0, regardless of the force field; however, the manual states that, with GROMOS force fields, one should use rvdw >= 1.4; which is correct ? Thank you in advance for your help JP Gri

Re: [gmx-users] water box with prescribed volume and density

rgy. See the manual, Appendix C. How many values in the .log > file are you looking at? Anything printed there is just an instantaneous > value, > and may not represent the actual average over the simulation. You're right; both give identical averages. rlist, rcoulomb an

Re: [gmx-users] water box with prescribed volume and density

fully equilibrated? Since the run lasted 50 mn on a signle node, I cans easily extend the equilibration. A last point is not clear; which file should I start from to extend the computation: .cpt, .trr, or .xtc? Thank you again for taking pains with an ignorant user JP Grivet -- gmx-users mailing lis

[gmx-users] water box with prescribed volume and density

molecules in the box, with an even lower density of 808 g/l. How should I proceed to get (approximately) the desired number and density? By the way, I notice that the number of molecules in topol.top is not updated; is that normal ? Thanks in advance for tour time and help JP Grivet -- gmx-users