Hi Yang, I am performing a simulation of a peptide in vacuum, and in the mailing archieve, I read that using of linear option of comm_mode in the vacuum simulations.
Is it due to the relatively rapid convergence of molecules in the vacuum environment? Thanks in advance Ozge -----Original Message----- From: Yang Ye <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> Date: Sun, 14 Oct 2007 03:42:12 -0700 (PDT) Subject: Re: [gmx-users] the comm_mode Generally, linear. For simulation in vacumm, you need rotation. With big molecules, equilibration may not be done thoroughly; this may result in very obivious rotation that Linear can not prevent. So visualize your trajectory and check your molecule. If it happens, you need to apply Rotation in the beginning of your simulation for a few ns. Regards, Yang Ye ----- Original Message ---- From: Dechang Li <[EMAIL PROTECTED]> To: gmx-users <[email protected]> Sent: Sunday, October 14, 2007 5:34:35 PM Subject: [gmx-users] the comm_mode Dear all, There are three options of comm_mode: Linear, Angular and none. The option Angular is said that "Remove center of mass translation and rotation around the center of mass". Does it mean the option Angular remove the translation and rotation BOTH ? If I want to do a simulation such as a protein in the explicit water, which option would be better? Or it will be the same? Thank you for your reply. Best regards, 2007-10-14 ========================================= Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] ========================================= _______________________________________________ gmx-users mailing list [email protected] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
