Ok, I don't quite understand something. My dowloaded pdb file of my molecule is centered at about 3 3 3 (in x y z, nm).
I perform genbox to solvate it: No problem. I then perform editconf to translate the center of the molecule to 0 0 0 (and move the water likewise): editconf -f Molecule_Solv.gro -o Molecule_Solv -translate -3 -3 -3 [Note here, I'm not using the -center option, b/c I want to place the center of the molecule, not the entire system, at 0 0 0]. No problem here (when I load the structure up in VMD and measure its geometric center, it is indeed at 0 0 0). But then, when I run a simulation on this structure (say a brief energy minimization), it reverts back to its original center at 3 3 3. In other words, the outputted structure after the minimization has the molecule centered back at 3 3 3. Why is this happening??? Does this have anything to do with the dimensions of the box? (which are 6 6 6). The dimensions are irrespective of the centering of the box, right? [I know this seems a little trivial. I'd like to have my molecule centered at 0 0 0, b/c I'll be collecting coordinates later and it'll just make my math easier.] > Arneh Babakhani wrote: >> Hi, >> >> I'm using editconf to center my sytem about the origin (0 0 0). No >> problem there. >> >> But then when I use genbox to solvate the resulting structure, the >> solvent >> is offset (not centered about 0 0 0). Is there a way to correct this? > > Have you tried editconf on the solvated structure? Why does it matter > anyway? > > Mark > _______________________________________________ > 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 > _______________________________________________ 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
