RE: [gmx-users] Using editconf to center on 0 0 0 , then using genbox
> [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.] You will have to do that centering after the simulation has been run and the trajectory files written. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org 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
Re: [gmx-users] Using editconf to center on 0 0 0 , then using genbox
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 listgmx-users@gromacs.org > 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 listgmx-users@gromacs.org 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
Re: [gmx-users] Using editconf to center on 0 0 0 , then using genbox
I'd like to have my structure centered on 0 0 0 . The solvated structure is completely off. My protein is at the center, but the solvation shell is way off center. I just dont understand why genbox isn't recognizing the previous editconf step. Ok, I'll try solvating first then using editconf. > 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 listgmx-users@gromacs.org > 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 listgmx-users@gromacs.org 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
Re: [gmx-users] Using editconf to center on 0 0 0 , then using genbox
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 listgmx-users@gromacs.org 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] Using editconf to center on 0 0 0 , then using genbox
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? Arneh ___ gmx-users mailing listgmx-users@gromacs.org 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
