Dear Mark and Justin, Thanks for very informative comments. I'll try to rotate and then solvate.
Paymon -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: October 18, 2010 7:26 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] editconf On 19/10/2010 12:22 PM, Payman Pirzadeh wrote: > After rotation, wouldn't a minimization with very very small steps solve the > problem? Only if the solute surface was very close to being symmetric about the rotation axis. Since that never happens, editconf doesn't even have the ability to try. Mark > Paymon > > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Mark Abraham > Sent: October 18, 2010 7:14 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] editconf > > On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote: >> Hello, >> I am trying to rotate my protein in my simulation box (solvent molecules >> are there as well). I issue the following command: >> editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15 >> 180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328 >> >> I select my group (protein) in the first group selection prompt and >> whole system as output in the second prompt. However, in the output file >> the whole system is rotated rather than protein only. Also, despite the >> -box switch used, the dimensions of the box changes. >> Is there any ideas on what I am missing in my procedure? > editconf can't rotate the solute with solvent present - what would you > like it to do about the voids and clashes that would be created? Do your > rotation before you solvate. > > Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
