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 gmx-users@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: [EMAIL PROTECTED] =___ gmx-users mailing listgmx-users@gromacs.org 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
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? Thanks in advance Ozge -Original Message- From: Yang Ye [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@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 [EMAIL PROTECTED] To: gmx-users gmx-users@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: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: Re: [gmx-users] the comm_mode
- Original Message From: OZGE ENGIN [EMAIL PROTECTED] To: [EMAIL PROTECTED]; gmx-users@gromacs.org Cc: gmx-users@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 [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@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 [EMAIL PROTECTED] To: gmx-users gmx-users@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: [EMAIL PROTECTED] =___ gmx-users mailing listgmx-users@gromacs.org 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
Re: Re: Re: [gmx-users] the comm_mode
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 [EMAIL PROTECTED] To: gmx-users@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 [EMAIL PROTECTED] To: [EMAIL PROTECTED]; gmx-users@gromacs.org Cc: gmx-users@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 [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@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 [EMAIL PROTECTED] To: gmx-users gmx-users@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: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] the comm_mode
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 [EMAIL PROTECTED] To: gmx-users@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 [EMAIL PROTECTED] To: [EMAIL PROTECTED]; gmx-users@gromacs.org Cc: gmx-users@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 [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@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 [EMAIL PROTECTED] To: gmx-users gmx-users@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: [EMAIL PROTECTED] = ___ gmx-users mailing listgmx-users@gromacs.org 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
