Hi, Read a bit more carefully though. A cubic box is based on the circumscribed sphere of the solute, dilated with the desired distance between the solute and the wall (and it has nothing to do with calculation of the solvation surface, which to me sounds to be related to solvent accessible surface).
And, yes, the three numbers at the end of the .gro file give the vector lengths for a rectangular unit cell (of which the cubic is the regular form). And you may at some point come to your senses and use a rhombic dodecahedron. And then you'll come to the user list again, asking what these nine numbers mean (which is also in the manual and in the archives of the list). And afterwards you'll try to visualize it and come with the question why your box doesn't show up as a rhombic dodecahedron, but rather as a rectangular (which is also explained in the manual, chapter three, and explained many times on the list). And you're bound to find your molecule sticking out of the solvent, but that's not an error because you use PBC, which really is in the manual and in the archives, as well as mentioned in the wiki. Now, please excuse me for being a bit harsh maybe. Yet, I do not need to answer at all, but I felt that the slight off-the-point reply regarding the setup of the box deserved an answer. And then, being writing already, I thought to anticipate some of the questions I see coming. Especially these questions where one gives the answer with a "right??" are a bit annoying, as that indicates that one is on the right track and capable of thinking logically, implying also that it shouldn't be a big mental leap to find the answer in one of the sources available. Tsjerk On Fri, Jul 4, 2008 at 11:33 AM, Nuno Azoia <[EMAIL PROTECTED]> wrote: > Chih-Ying Lin wrote: >> >> Hi >> >> 1. in the last row of .gro file, the three number represent the length >> of the box on X, Y , and Z directions in nanometer. >> Right?? >> > > These values represents the real dimensions of the box >> >> 2. for the editconf command, >> editconf -d Distance_between_the_solute_and_the_box bt cubicsur >> Right?? >> >> > > In this case the program takes the solute and calculates the solvation > surface. From this calculates the maximum size of this surface, add twice > the value "Distance_between_the_solute_and_the_box" (distance in the left > side and distance in the right side), and the total value is, in the case of > cubic box, the size of each direction of the box (X=Y=Z). > > Some careful reading of the Manual will help. > > >> >> what are the differences between the three number in the .gro file and >> the distance in the editconf command ?? >> >> Thanks >> Lin >> _______________________________________________ >> 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 >> >> > > > -- > > Nuno Gonçalo Azoia Lopes > > Laboratório de Investigação em Acabamento > Departamento de Engenharia Têxtil > Universidade do Minho > Campus de Azurém > 4800-058 Guimarães > Portugal > > Tel: +351 253 510 280 - Ext: 517 289 > Fax: +351 253 510 293 > > Mobile: +351 965 382 487 > E-mail: [EMAIL PROTECTED] > > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
