RE: [gmx-users] genion doesn't work in 4.6.1?
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 listgmx-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 listgmx-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
RE: Fw: [gmx-users] water molecule can not be settled
After having followed for longer time the queries sent by some Indian fellows, I wonder if it wouldn't more effective to arrange for a GROMACS tutorial offered by Justin in an Indian location. Maybe you, the Indian fellows, can arrange for the financing and invite Justin to hold such a Tutorial on the basics of MD simulations and their implementation in GROMACS. Considering the time Justin is spending responding to your queries, maybe because you are devoid of adequate supervision or theoretical background, this would be only fair. This posting is maybe a little bit off topic, but somehow related. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Friday, April 05, 2013 5:22 PM To: Discussion list for GROMACS users Subject: Re: Fw: [gmx-users] water molecule can not be settled You mean start over the NPT step? Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, April 5, 2013 7:50 PM Subject: Re: Fw: [gmx-users] water molecule can not be settled On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh wrote: > As I visualized the system, I see a water molecule somewhere between lipid > chains near the protein entrance. This has been happen during NPT. I' d > like to delete this molecule but with such a kind of fatal error this would > impossible. So what's the way? Is there any tricky way to change > coordinate of molecule? but I seems also impossible becasue PME problem! > So whats the solution? > > Delete the molecule, adjust your topology (and index file, if necessary), and start over with the equilibration. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
RE: [gmx-users] Index file
A good minded advice Shima: think more for your self; science is not easy, or if it's not possible, ask ur adviser, or look for a new job. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Monday, December 31, 2012 5:58 PM To: Justin Lemkul; Discussion list for GROMACS users Subject: Re: [gmx-users] Index file These are the last line of my gro file: 5SOLHW299818 7.429 8.372 11.524 5CL CL99819 0.485 3.864 11.451 5CL CL99820 5.689 6.730 9.692 9.21490 8.92980 12.40750 Here, I brought you the output of make_ndx command. As you see CL ions are not recognized here. Analysing residue names: There are:48Protein residues There are: 238 Other residues There are: 12624 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 99817 atoms 1 Protein : 720 atoms 2 Protein-H : 356 atoms 3 C-alpha :48 atoms 4 Backbone: 144 atoms 5 MainChain : 190 atoms 6 MainChain+Cb: 234 atoms 7 MainChain+H : 240 atoms 8 SideChain : 480 atoms 9 SideChain-H : 166 atoms 10 Prot-Masses : 720 atoms 11 non-Protein : 99097 atoms 12 Other : 31892 atoms 13 POPC: 31892 atoms 14 Water : 67205 atoms 15 SOL : 67205 atoms 16 non-Water : 32612 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom& 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char "name": group'case': case sensitive 'q': save and quit 'ri': residue index Somehow confusing for me! Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Monday, December 31, 2012 8:19 PM Subject: Re: [gmx-users] Index file On 12/31/12 11:45 AM, Shima Arasteh wrote: > > > It is 4.5.5. > I need to say that I had a pdb file which was produced by VMD, May it be the > reason of problem? > > Without seeing the aforementioned information (substituting make_ndx screen output for editconf command, which is not relevant), it's impossible to say anything. There is no logical reason why ions present in the coordinate file (independent of format) do not show up in the selection list and I cannot reproduce the problem with any file I have available. Ions are showing up just fine in everything I can see. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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 listgmx-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
