<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV>Generally, linear. For simulation in vacumm, you need rotation.</DIV>
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<DIV>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.<BR> </DIV>Regards,<BR>Yang Ye
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: Dechang Li <li.dc06@gmail.com><BR>To: gmx-users <gmx-users@gromacs.org><BR>Sent: Sunday, October 14, 2007 5:34:35 PM<BR>Subject: [gmx-users] the comm_mode<BR><BR>
<DIV>Dear all,<BR> <BR> There are three options of comm_mode: Linear, Angular and none. <BR>The option Angular is said that "Remove center of mass translation <BR>and rotation around the center of mass". Does it mean the option<BR>Angular remove the translation and rotation BOTH ? <BR> If I want to do a simulation such as a protein in the explicit<BR>water, which option would be better? Or it will be the same?<BR> Thank you for your reply.<BR> <BR><BR>Best regards,<BR><BR>2007-10-14<BR> <BR><BR>========================================= <BR>Dechang Li, PhD Candidate<BR>Department of Engineering Mechanics<BR>Tsinghua University<BR>Beijing 100084<BR>PR China <BR><BR>Tel: +86-10-62773779(O) <BR>Email:
li.dc06@gmail.com<BR>=========================================</DIV></DIV><BR></DIV></div></body></html>