Again and again posting from Abhishek Acharya or Shima, or Rama David or somehow else ... pls read my posting before, it could be useful for you, Indian fellows ... maybe it's possible to get some kind of agreement though brahmin.net or so ..
Best regards of somebody experienced with Indian "science" Best, Felipe ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Abhishek Acharya [aacha...@iitk.ac.in] Sent: Friday, April 05, 2013 9:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] genion doesn't work in 4.6.1? > On 04/05/2013 09:09 PM, Warren Gallin wrote: >> Don't you have to give tyne name of the positive and negative ions that >> will be added by genion? Otherwise, how would it know? >> >> Warren Gallin > > No, it doesn't work either: > > genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral > -norandom -pname NA -nname CL > > or > > genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral > -norandom -pname NA -pq 11 > > Reading file ions.tpr, VERSION 4.6.1 (single precision) > Using a coulomb cut-off of 1.2 nm > No ions to add and no potential to calculate. > You are using the wrong combinations of flags: Either of the following should do the job: genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -pname NA -np 11 -pq 1 or genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -conc 0.15 -neutral (incase you want a NaCl conc of 0.15 M. Only in this case, genion will automatically add NA and CL ions to neutralize the charge and sufficiently reach the given conc., in this case 0.15 M) Cheers. Abhishek Acharya Structural and Computational Biology Lab Indian Institute of Technology Kanpur -- 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
