<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt">Use trjconv -ur compact before visualizing it but don't use those files for MD.<br><div> </div>Regards,<br>Yang Ye<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Rui Li <moonfine@mail.sdu.edu.cn><br>To: gmx-users@gromacs.org<br>Sent: Wednesday, July 4, 2007 10:12:17 AM<br>Subject: Re: [gmx-users] about truncated octahedral periodic box<br><br><div>Hi Yangye and Tsjerk,<br><br>Thank you for your reply.<br><br>I have used -c to center the molecule.<br><br>So it just seem to uncenter in visualizer. However, it will not influence the MD,<br>right?<br><br><br>在您的来信中曾经提到:<br>>From: Yang Ye <leafyoung@yahoo.com><br>>Reply-To:
Discussion list for GROMACS users <gmx-users@gromacs.org><br>>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>>Subject: Re: [gmx-users] about truncated octahedral periodic box<br>>Date:Wed, 04 Jul 2007 09:53:23 +0800<br>><br>>On 7/3/2007 9:11 PM, Tsjerk Wassenaar wrote:<br>> > Hi Yang Ye,<br>> ><br>> > It was a different question; the question Rui Li asked was "why is my<br>> > protein not in the center of my truncated octahedron"?.<br>> ><br>> > The answer to that question is not:<br>> >> You shall use trjconv -ur compact -pbc atom to transform your model.<br>> > but is more fundamentally related to understanding the principles of<br>> > periodic boundary conditions (rather than to the use of trjconv).<br>> Thanks for the note, Tsjerk.<br>> <br>> There could be several possible reasons:<br>> The first reason could be that Li didn't run trjconv -ur
compact. What <br>> is visible in any visualizer is a cuboid with protein not in the center. <br>> This while can be solved technically, is actually related how non-cubic <br>> box type is represented in gromacs.<br>> <br>> The second reason could be when specifying the box type with editconf, <br>> molecule is not centered with -c. And Li actually used trjconv -ur <br>> compact to convert the molecule before visualizing it.<br>> <br>> All in all, it is a very good practice to visualize the system before <br>> running it.<br>> ><br>> >> This is my second time in the week answering this question.<br>> > I know.., I get the same feeling now and then.., but keep keen on<br>> > reading the question asked.<br>> ><br>> > Cheers,<br>> ><br>> > Tsjerk<br>> ><br>> <br>> _______________________________________________<br>> gmx-users mailing
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