On 31.05.2010, at 17:37, grivet wrote: > 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 is an annealing from the previous temperature to the next one, >>>> using a NPT ensemble. Using the result of that, I run an NVT simulation. >>>> >>>> Where can I recover the box average box dimensions, volume and density >>>> of water in the NVT run ? >>> >>> Use g_energy. > Appaerently no; g_energy gives me a choice of 37 variables to print > (energies, pressure tensor, virial, etc..) but not box dimensions, > volume or density. Is this because I am using 4.0.5 ? No this is because you are simulating NVT, so you know your box dimensions.
/Flo >> >> I should also add that under an NVT ensemble, none of these values will have >> changed from whatever the initial conditions were. Only under the influence >> of >> pressure coupling does the density vary (since the box vectors fluctuate). >> Volume is constant by virtue of the fact that you're using NVT. >> >> -Justin >> >>>> 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 > My mistake. g_density outputs *partial* densities, with a default number > of slices = 50. Setting -sl 0 recovers a single normal density. >>> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
PGP.sig
Description: This is a digitally signed message part
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
