After rotation, wouldn't a minimization with very very small steps solve the problem?
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