<DIV>Dear Mark,</DIV>
<DIV> Thank you for your reply. It seems reasonable to deal with a frame at one time. But in my code, the coordinates in two different frames are frequently required to compare to each other. Other part of this code is like g_msd which calculates the mean-squared displacements for the atoms satisfied with the conditions. So, first of all, I had better save the coordinates in the 2D-arrays using xdrfile. I do not find such a tool in gmx that can realize it. Is there any other algorithms to do so more effectively? Please provide more detail about it.</DIV>
<DIV>Yours sincerely,</DIV>
<DIV>Chaofu Wu, Dr.</DIV>
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<DIV id=menu_sender><B>发件人:</B> "Mark Abraham"<Mark.Abraham@anu.edu.au>;</DIV>
<DIV><B>发送时间:</B> 2010年11月29日(星期一) 晚上7:38</DIV>
<DIV><B>收件人:</B> "Discussion list for GROMACS users"<gmx-users@gromacs.org>; <WBR></DIV>
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<DIV><B>主题:</B> Re: [gmx-users] How to save the coordinates of all atoms inthe 2D-arrays using xdrfile?</DIV></DIV>
<DIV> </DIV>On 28/11/2010 12:12 AM, 英雄不再寂寞 wrote:<BR>> Dear gmxers,<BR>> I am trying to perform an analysis on the trjectory file using xdrfile <BR>> library. First of all, I want to save the coordinates of all atoms in <BR>> three 2D-arrays, i.e. xx[step-1][natom-1], yy[step-1][natom-1], <BR>> zz[step-1][natom-1]. How to do so? Could you give me some hints, <BR>> please? If you had happened to do so, could you kindly send the code <BR>> to me? Thanks a lot.<BR>> Yours sincerely,<BR>> Chaofu Wu, Dr.<BR><BR>You probably don't want to do that, because it doesn't scale to large <BR>numbers of trajectory frames - you will run out of memory eventually. If <BR>at all possible you should structure your algorithm to deal with one <BR>frame at a time. There are already GROMACS functions that make that <BR>easy. Pick a GROMACS trajectory analysis tool that sounds fairly simple <BR>and vaguely similar to what you want to do, and look at how its code works.<BR><BR>Mark<BR>-- <BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR></DIV></includetail></DIV>