Thank you very much, it is very helpful for me.<br><br>nslam<br><br><b><i>Yang Ye <leafyoung@yahoo.com></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> On 7/3/2007 2:24 AM, Lam Nguyen Sy wrote:<br>> Dear all,<br>><br>> I am new to Gromacs, and I am trying to simulate my<br>> systems with octahedral box type (the option I used<br>> for editconf was "-bt octahedral"). <br>> I need to know what type of box that Gromacs put the<br>> output systems in, because I am trying to do some<br>> translations on some molecules that are outside the<br>> box to put them inside, so that I can correctly<br>> compute the number of contacts.<br>> When using VMD to visualize some output .gro or .pdb<br>> files, I just saw a rectangular box. Furthermore, it<br>> is said on page 12 of the GROMACS User Manual version<br>> 3.3 that "Even when simulating using a triclinic
box,<br>> GROMACS always puts the particles in a brick shaped<br>> volume, for efficiency reason" and "So from the output<br>> trajectory it might seem like the simulation was done<br>> in a rectangular box." I am not clear on this point. <br>> There is a series of numbers at the end of my .gro<br>> files:<br>> 4.12763 3.89157 3.37019 0.00000 0.00000 <br>> 1.37588 0.00000 -1.37588 1.94578<br>> I guess they are the components of the box vectors.<br>> <br>Gromacs always output the type of box you have choosen. Because VMD <br>doesn't support octahedral-type of box, it simply read the first three <br>numbers and set them for x-, y-, and z-dimensions. You need to use <br>"trjconv -ur compact -pbc atom" to convert your trajectory as well as <br>your gro or pdb file to get them correctly displayed.<br>> What type of box does GROMACS usually put an output<br>> system in? And in the case of my systems, what is the<br>> type of
box containing them in the output files?<br>><br>> Any help would be very useful. Thank you in advanced.<br>><br>> Nguyen Sy Lam<br>><br>><br>> <br>> ____________________________________________________________________________________<br>> Finding fabulous fares is fun. <br>> Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains.<br>> http://farechase.yahoo.com/promo-generic-14795097<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br>><br>>
<br><br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br></blockquote><br><p> 
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