Re: [gmx-users] nstcomm < nstcalenergy
On 8/29/17 1:47 AM, Simon Kit Sang Chu wrote: Dear every user, I am using Andersen thermostat and nstcomm should be set to 1 (step). However, after specifying nstcomm = 1, an error has returned - nstcalenergy cannot be smaller than nstcomm. GROMACS automatically sets it to nstcalenergy step. I fail to search for "nstcalenergy" in neither mdp nor manual. It's there, and has been for several years: http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#output-control If you're using an algorithm that requires global summation of energy terms, or otherwise limited by algorithmic requirements as you are here, you have to sum the energies at every step. This slows things down, but in some cases (like yours) it's required. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] nstcomm < nstcalenergy
Hi， Firstly, you should confirm your gromacs version, gromacs 5.x certainly includes nstcalenergy options in .mdp file. So you must set nstcalenergy=1 while the default value is 10 in .mdp if you want to nstcomm=1. thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] nstcomm < nstcalenergy
Dear every user, I am using Andersen thermostat and nstcomm should be set to 1 (step). However, after specifying nstcomm = 1, an error has returned - nstcalenergy cannot be smaller than nstcomm. GROMACS automatically sets it to nstcalenergy step. I fail to search for "nstcalenergy" in neither mdp nor manual. I am asking again since I did not receive any reply on my previous post. Sorry for my annoyance. Regards, Simon -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
