[From nobody Mon Jun 4 13:16:43 2018 Date: Mon, 04 Jun 2018 13:52:25 +0530 Message-ID: <20180604135225.Horde.puzSdvZUgEDBtQGfw8Db6A1@mailweb.iacs.res.in> From: spss4@iacs.res.in To: gmx-users@gromacs.org Subject: Centering the molecule Received: from proxy.iacs.res.in (proxy.iacs.res.in [192.168.150.105]) by mailweb.iacs.res.in (Horde Framework) with HTTP; Mon, 04 Jun 2018 13:52:25 +0530 User-Agent: Internet Messaging Program (IMP) H5 (6.2.1) Content-Type: multipart/alternative; boundary="=_q5dqDW4Xyr6Y3JYC9zjUzQ4" MIME-Version: 1.0 This message is in MIME format. --=_q5dqDW4Xyr6Y3JYC9zjUzQ4 Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes Content-Description: Plaintext Message Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi all I want to center my molecule into a rectangular box by GROMACS. I am using the following command: gmx trjconv -f=C2=A0 traj.trr -s md.tpr -center -pbc=C2=A0 mol -b 100 -e 12= 0 -o=C2=A0 test.gro=C2=A0 But output=C2=A0 shown is still out of the box. This command works for cubi= c box.=C2=A0Is there anything different flag for=C2=A0rectangular box? My box= size is 5 5 7. Thanks Sunipa --=_q5dqDW4Xyr6Y3JYC9zjUzQ4 Content-Type: text/html; charset=UTF-8 Content-Description: HTML Message Content-Disposition: inline <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd"> <html><head><meta http-equiv="content-type" content="text/html; charset=UTF-8"></head><body style="font-family:Arial;font-size:14px"><p>Hi all<br> I want to center my molecule into a rectangular box by GROMACS. I am using the following command:<br> gmx trjconv -f&nbsp; traj.trr -s md.tpr -center -pbc&nbsp; mol -b 100 -e 120 -o&nbsp; test.gro&nbsp;<br> But output&nbsp; shown is still out of the box. This command works for cubic box.&nbsp;Is there anything different flag for&nbsp;rectangular box? My box size is 5 5 7.<br><br> Thanks<br> Sunipa<br></p></body></html> --=_q5dqDW4Xyr6Y3JYC9zjUzQ4-- ]