[gmx-users] the comm_mode

[Yang Ye]

Hi,

It's about geometry.

Be pragmatic. By inspecting the trajectory, you can which one works. if 
Linear works for your system, use it; otherwise, use rotation. Although 
I prefer to use Rotation for simulations in vacuum in the first place, 
and for first few ns simulation for big protein with explicit solvent.

Regards,
Yang Ye

On 10/15/2007 12:24 AM, OZGE ENGIN wrote:
> Sorry, but I have to ask some more questions. I have just started to perform simulations in vacuum. I can understand not using of PME in vacuum simulations; however, I can not understand the sentence you wrote :
> 'rotation is recomended.' COM velocity removal's effect is directly visible.
> Is it related to conservation of angular momentum?
>
> Thank you very much!
>
> Oz.
> -----Original Message-----
> From: Yang Ye <leafyoung at yahoo.com>
> To: gmx-users at gromacs.org
> Date: Sun, 14 Oct 2007 07:07:18 -0700 (PDT)
> Subject: Re: Re: [gmx-users] the comm_mode
>
> ----- Original Message ----
> From: OZGE ENGIN <OZENGIN at KU.EDU.TR>
> To: leafyoung at yahoo.com; gmx-users at gromacs.org
> Cc: gmx-users at gromacs.org
> Sent: Sunday, October 14, 2007 8:33:28 PM
> Subject: Re: Re: [gmx-users] the comm_mode
>
>
> 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?
>
>   
>>> It is not because of this reason, it is due to PBC. Simulation in vacuum is usually done without PBC, Rotation is recommended.
>>> COM velocity removal's effect is directly visible, so if "Linear" works for you, you may use it.
>>>       
>
> Thanks in advance 
>
> Ozge
>
> -----Original Message-----
> From: Yang Ye <leafyoung at yahoo.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> 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 <li.dc06 at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> 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: li.dc06 at gmail.com
> =========================================
>
>
>
>
>