[gmx-users] What's the default pbc of Gromacs trajectories?
Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was whole, which means no broken molecules. But I just found it's not the case for the latest version, since I can see broken lipids for my membrane system using ngmx. I'm just wondering what's the default pbc for the latest Gromacs version and whether there is a way to change it before MD simulations. Thanks for your help. Lanyuan Lu _ MSN 中文网，最新时尚生活资讯，白领聚集门户。 http://cn.msn.com ___ 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] What's the default pbc of Gromacs trajectories?
LuLanyuan wrote: Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was whole, which means no broken molecules. But I just found it's not the case for the latest version, since I can see broken lipids for my membrane system using ngmx. I'm just wondering what's the default pbc for the latest Gromacs version and whether there is a way to change it before MD simulations. I think you are asking two separate questions. From trjconv -h you can find the default behavior for PBC treatment, which is none, as in, leave the coordinates alone. The PBC behavior of an MD simulation is specified in the .mdp file. Removal of PBC from broken starting structures should be the first step in the simulation. -Justin Thanks for your help. Lanyuan Lu _ MSN 中文网，最新时尚生活资讯，白领聚集门户。 http://cn.msn.com ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] What's the default pbc of Gromacs trajectories?
Thanks for your reply. I just checked the online manual for .mdp. But I didn't find an option to change output pbc types. If I need the output trr file to be whole as that from an older version, can I set it up anywhere? I understand I can use trjconv to convert trr files. But usually trr files are huge and the convertion takes time. Thanks, Lanyuan Lu Date: Mon, 28 Jul 2008 17:07:30 -0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] What's the default pbc of Gromacs trajectories? LuLanyuan wrote: Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was whole, which means no broken molecules. But I just found it's not the case for the latest version, since I can see broken lipids for my membrane system using ngmx. I'm just wondering what's the default pbc for the latest Gromacs version and whether there is a way to change it before MD simulations. I think you are asking two separate questions. From trjconv -h you can find the default behavior for PBC treatment, which is none, as in, leave the coordinates alone. The PBC behavior of an MD simulation is specified in the .mdp file. Removal of PBC from broken starting structures should be the first step in the simulation. -Justin Thanks for your help. Lanyuan Lu _ MSN 中文网，最新时尚生活资讯，白领聚集门户。 http://cn.msn.com ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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 _ Windows Live Photo gallery 数码相机的超级伴侣，轻松管理和编辑照片，还能制作全景美图！ http://get.live.cn/product/photo.html___ 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] What's the default pbc of Gromacs trajectories?
LuLanyuan wrote: Thanks for your reply. I just checked the online manual for .mdp. But I didn't find an option to change output pbc types. If I need the output trr file to be whole as that from an older version, can I set it up anywhere? What you are probably seeing is a visualization artifact, but you haven't described things very thoroughly. In fact, mdrun does not write broken molecules; everything should be whole. Like I said before, as soon as you start a simulation, all broken molecules are made whole. Such behavior is defined in the topology. If there is a bond between two atoms at a given distance, mdrun knows these atoms are bonded, even if they initially appear across the box from each other. I understand I can use trjconv to convert trr files. But usually trr files are huge and the convertion takes time. So write your output in .xtc format. Use the nstxtcout option in the .mdp file. -Justin Thanks, Lanyuan Lu Date: Mon, 28 Jul 2008 17:07:30 -0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] What's the default pbc of Gromacs trajectories? LuLanyuan wrote: Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was whole, which means no broken molecules. But I! ! just found it's not the case for the latest version, since I can see broken lipids for my membrane system using ngmx. I'm just wondering what's the default pbc for the latest Gromacs version and whether there is a way to change it before MD simulations. I think you are asking two separate questions. From trjconv -h you can find the default behavior for PBC treatment, which is none, as in, leave the coordinates alone. The PBC behavior of an MD simulation is specified in the .mdp file. Removal of PBC from broken starting structures should be the first step in the simulation. -Justin Thanks for your help. Lanyuan Lu _ MSN 中文网，最新时尚生活资讯，白领聚集门户。 http://cn.msn.com ! ! ___ gmx-users mailing list gmx-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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing list gmx-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 用 Windows Live Spaces 展示个性自我，与好友分享生活！ 了解更多信息！ http://spaces.live.com/?page=HP -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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
