You can modify your original top's [ molecules ] section to make it only contains the protein.
On 8/6/2007 4:36 PM, [EMAIL PROTECTED] wrote: > > ----- 原文 ----- > Dear Yang Ye > Thank you very much for your advice! > Is any special requirement for this mdp file in step 2 when I make > a tpr file? > Best regards! > Paul > > *From:* Yang Ye <mailto:[EMAIL PROTECTED]> > *To:* Discussion list for GROMACS users > <mailto:[email protected]> > *Subject:* Re: [gmx-users] potential energy of specific group > *Sent:* Sun Aug 05 21:47:55 CST 2007 > > > > > Hi, > > You shall > > 1. Extract the protein coordinates (use trjconv and select groups) > from > your trajectory file (.xtc). > 2. Make a .tpr file which only contains protein. > 3. Use mdrun -rerun to process the trajectory file obtained from 1. > > Regards, > Yang Ye > > On 8/5/2007 4:28 PM, [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> wrote: > > > > Hi all, > > > > I am a freshman in using gromacs. According to my unstanding, the > > "potential" in g_energy > > > > indicates the system's potential energy. Now I want to know the > > potential energy of a specific > > > > group, such as the protein. How should I get it? Could anybody > give me > > any help ? Thanks a lot! > > > > Paul > > > > > > > > > ------------------------------------------------------------------------ > > 我积分，我得奖，天天乐透！ > > <http://goto.mail.sohu.com/goto.php3?code=mailadt-ta1> > > *用搜狗拼音写邮件，体验更流畅的中文输入>> > > <http://goto.mail.sohu.com/goto.php3?code=mailadt-ta> > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > <mailto:[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] > <mailto:[EMAIL PROTECTED]>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > gmx-users mailing list [email protected] > <mailto:[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] > <mailto:[EMAIL PROTECTED]>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ------------------------------------------------------------------------ > 我积分，我得奖，天天乐透！ > <http://goto.mail.sohu.com/goto.php3?code=mailadt-ta1> > *用搜狗拼音写邮件，体验更流畅的中文输入>> > <http://goto.mail.sohu.com/goto.php3?code=mailadt-ta> > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 _______________________________________________ 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
