Re: [gmx-users] Centering the system
I used -fit or boxcenter or trans or .. any other thing which I though to solve my problem, but did not work. Would you give me a hint pleaaasssee? Thanks a lot. Sincerely, Shima On Wednesday, October 16, 2013 4:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/16/13 8:29 AM, Shima Arasteh wrote: Dear gmx users, I have a system consist of a lipid bilayer and a peptide. As the initial configuration, the peptide is located in center of the x-y plane above lipid bilayer. After running MD, the peptide shows interactions with the polar groups. It's ok, but the peptide is near one edge of the x-y plane of the bilayer. I' d like to know if there is any way to use the properties of the pbc and see the peptide in center of the x-y plane while interacting with the polar groups? trjconv has a number of ways to deal with this. Please read trjconv -h. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Centering the system
Dear gmx users, I have a system consist of a lipid bilayer and a peptide. As the initial configuration, the peptide is located in center of the x-y plane above lipid bilayer. After running MD, the peptide shows interactions with the polar groups. It's ok, but the peptide is near one edge of the x-y plane of the bilayer. I' d like to know if there is any way to use the properties of the pbc and see the peptide in center of the x-y plane while interacting with the polar groups? Thanks in advance, Your suggestions would be appreciated. Sincerely, Shima -- 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] Umbrella Sampling PMF
Hi, I ran US on an ion through a channel inserted in a bilayer. I used g_wham and got the profile output. In the visualized profile, I see a region that the plot shows a flat line and it seems the data is missed there. Would you please let me know what the reason of missing data is? Thanks for your suggestions in advance. Sincerely, Shima -- 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] Distribution of an atom along a trajectory
Hi, As I know, g_spatial gives me the spatial distribution of a specified group. If there is any tool to give me the planar distribution of group in x-y graph? Or if there is any command to help me? Thanks in advance for your help. I appreciate you. Sincerely, Shima -- 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] position restraint
Hi, I want to put position restraint on an ion , First made an .itp file of the ion: posre_ion.itp Then added these line to top file: #include ./charmm36-modified.ff/ions.itp #ifdef POSRES_ION #include ion_posre.itp #endif And added the line to mdp file define = -DPOSRES_ION But the grompp failed because it gives me the fatal error that the include line is not in the correct position. Would you please let me know if the inclusion of posre_ion.itp is not as I did? What's the problem? Thanks in advance for your suggesions. Sincerely, Shima -- 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] position restraint
yes, but there was only a typing mistake in my earlier email. The error I get still exists when I use the correct itp file: First made an .itp file of the ion: ion_posre.itp Then added these line to top file: #include ./charmm36-modified.ff/ions.itp #ifdef POSRES_ION #include ion_posre.itp #endif And added the line to mdp file define = -DPOSRES_ION Sincerely, Shima From: Gaurav Goel gauravgoel...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, August 22, 2013 3:39 PM Subject: Re: [gmx-users] position restraint One quick observation-- you mention the filename as posre_ion.itp, but are using ion_posre.itp at #include. -g On Thu, Aug 22, 2013 at 4:24 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Hi, I want to put position restraint on an ion , First made an .itp file of the ion: posre_ion.itp Then added these line to top file: #include ./charmm36-modified.ff/ions.itp #ifdef POSRES_ION #include ion_posre.itp #endif And added the line to mdp file define = -DPOSRES_ION But the grompp failed because it gives me the fatal error that the include line is not in the correct position. Would you please let me know if the inclusion of posre_ion.itp is not as I did? What's the problem? Thanks in advance for your suggesions. Sincerely, Shima -- 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 -- Gaurav Goel, PhD Assistant ProfessorDepartment of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India -- 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] position restraint
Yes, But the part in which the ions are introduced is #include ./charmm36-modified.ff/ions.itp , Is this not the right place to write the posre_ion lines? As I see it is in agreement with Atom index n in position_restraints out of bounds link. So what would be the solution? I don't see any itp file generated by pdb2gmx, for the ions such as chain A and other moleculetypes ? Would you give me a hint and help me with it please? Sincerely, Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Thu, 22 Aug 2013 03:54:07 -0700 (PDT) Subject: [gmx-users] position restraint To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, I want to put position restraint on an ion , First made an .itp file of the ion: posre_ion.itp Then added these line to top file: #include ./charmm36-modified.ff/ions.itp #ifdef POSRES_ION #include ion_posre.itp #endif And added the line to mdp file define = -DPOSRES_ION But the grompp failed because it gives me the fatal error that the include line is not in the correct position. Would you please let me know if the inclusion of posre_ion.itp is not as I did? What's the problem? Thanks in advance for your suggesions. Sincerely, Shima -- 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 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] position restraint
So I made a specific ces.itp file, and made a separate section in top file : ces.itp file: [ moleculetype ] ; molname nrexcl Ces 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CES 1 Ces Ces 1 1 .top file: ; Include topology for ces #include ces.itp #ifdef POSRES_ION #include posre_ion.itp #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp The posre_ion.itp file contains: ; position restraints for a_85563 of system [ position_restraints ] ; i funct fcx fcy fcz 85563 1 10 10 10 But it doesnt work, would you please let me know if I had a mistake? Thanks for your suggestions in earlier messages. Sincerely, Shima - Original Message - From: Mark Abraham mark.j.abra...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, August 22, 2013 5:54 PM Subject: Re: [gmx-users] position restraint Have a look at that file. It defines the [moleculetype] for lots of ions, but you need a position restraint that applies to whichever [moleculetype] is the one you want to use. That means it has to come before the next [moleculetype]. As manual 5.7 says, the .top format is hierarchical. So you need to modify the ions.itp, or make one that has only the ion of interest. Mark On Thu, Aug 22, 2013 at 3:01 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Yes, But the part in which the ions are introduced is #include ./charmm36-modified.ff/ions.itp , Is this not the right place to write the posre_ion lines? As I see it is in agreement with Atom index n in position_restraints out of bounds link. So what would be the solution? I don't see any itp file generated by pdb2gmx, for the ions such as chain A and other moleculetypes ? Would you give me a hint and help me with it please? Sincerely, Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Thu, 22 Aug 2013 03:54:07 -0700 (PDT) Subject: [gmx-users] position restraint To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, I want to put position restraint on an ion , First made an .itp file of the ion: posre_ion.itp Then added these line to top file: #include ./charmm36-modified.ff/ions.itp #ifdef POSRES_ION #include ion_posre.itp #endif And added the line to mdp file define = -DPOSRES_ION But the grompp failed because it gives me the fatal error that the include line is not in the correct position. Would you please let me know if the inclusion of posre_ion.itp is not as I did? What's the problem? Thanks in advance for your suggesions. Sincerely, Shima -- 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 -- 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] position restraint
If you mean that I need to modify the posre_ion.itp file to: ; position restraints for a_85563 of system [ position_restraints ] ; i funct fcx fcy fcz 1 1 10 10 10 It doesnt work.. :-( Sincerely, Shima - Original Message - From: Mark Abraham mark.j.abra...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, August 22, 2013 6:37 PM Subject: Re: [gmx-users] position restraint Now you have a [moleculetype] with one atom and hopefully a position restraint. But its [position_restraints] wants to act on atom 85563 of the molecule, which does not exist! See newly updated http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds Mark On Thu, Aug 22, 2013 at 3:58 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: So I made a specific ces.itp file, and made a separate section in top file : ces.itp file: [ moleculetype ] ; molname nrexcl Ces 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CES 1 Ces Ces 1 1 .top file: ; Include topology for ces #include ces.itp #ifdef POSRES_ION #include posre_ion.itp #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp The posre_ion.itp file contains: ; position restraints for a_85563 of system [ position_restraints ] ; i funct fcx fcy fcz 85563 1 10 10 10 But it doesnt work, would you please let me know if I had a mistake? Thanks for your suggestions in earlier messages. Sincerely, Shima - Original Message - From: Mark Abraham mark.j.abra...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, August 22, 2013 5:54 PM Subject: Re: [gmx-users] position restraint Have a look at that file. It defines the [moleculetype] for lots of ions, but you need a position restraint that applies to whichever [moleculetype] is the one you want to use. That means it has to come before the next [moleculetype]. As manual 5.7 says, the .top format is hierarchical. So you need to modify the ions.itp, or make one that has only the ion of interest. Mark On Thu, Aug 22, 2013 at 3:01 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Yes, But the part in which the ions are introduced is #include ./charmm36-modified.ff/ions.itp , Is this not the right place to write the posre_ion lines? As I see it is in agreement with Atom index n in position_restraints out of bounds link. So what would be the solution? I don't see any itp file generated by pdb2gmx, for the ions such as chain A and other moleculetypes ? Would you give me a hint and help me with it please? Sincerely, Shima -- Forwarded message -- From: Shima Arasteh shima_arasteh2...@yahoo.com Date: Thu, 22 Aug 2013 03:54:07 -0700 (PDT) Subject: [gmx-users] position restraint To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, I want to put position restraint on an ion , First made an .itp file of the ion: posre_ion.itp Then added these line to top file: #include ./charmm36-modified.ff/ions.itp #ifdef POSRES_ION #include ion_posre.itp #endif And added the line to mdp file define = -DPOSRES_ION But the grompp failed because it gives me the fatal error that the include line is not in the correct position. Would you please let me know if the inclusion of posre_ion.itp is not as I did? What's the problem? Thanks in advance for your suggesions. Sincerely, Shima -- 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 -- 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] g_WHAM
Hi, I have a tpr-files.dat containing 5 tpr files as it: 4.tpr 5.tpr 6.tpr 7.tpr 8.tpr Also the pullf-files.dat is in accordance with tpr-files.dat. But when I run g_wham and visualize the histo output, I see only one curve and not 4 curves which are expected to have appropriate overlaps! Would you please let me know how come? Is it usual to get one curve from each histo.xvg? Thanks for your suggestions. I appreciate you in advance. Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, August 8, 2013 11:08 PM Subject: Re: [gmx-users] g_WHAM On 8/8/13 2:37 PM, Shima Arasteh wrote: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCalvv It's the error what get; File input/output error: tpr-files.dat Then a file named tpr-files.dat does not exist in the working directory. Check for typos and the existence of the file. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, August 8, 2013 10:45 PM Subject: Re: [gmx-users] g_WHAM On 8/8/13 2:13 PM, Shima Arasteh wrote: Hi, Would you please let me know if it is possible to get just the first 2 histograms of total 24 histograms by running g_WHAM? I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling simulations and not the all. I ran such dat file, but doesn't work and gives me an error of no input file. The exact error, copied and pasted from the terminal, is more useful. g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal As long as pullf-files.dat and tpr-files.dat both specify the same number of input files and the .tpr and .xvg files therein match, there should be no problem. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] g_wham -sym
Thanks, I defined a new 0.0 position by -zprof0, and shifted the profile energy to a new 0.0. # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -zprof0 -1.081898 -sym But -sym gets me an error: Fatal error: Cannot symmetrize profile around z=0 with min=-1.312664 and max=-1.081898 Why does the g_wham tries to still symmetrize the profile around z=0? Would you please give me any suggestion? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, August 9, 2013 2:40 PM Subject: Re: [gmx-users] g_wham -sym On 8/9/13 5:48 AM, Shima Arasteh wrote: Hi, I use the g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Use -zprof0. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] g_wham -sym
Hi, I use the g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kca -sym I' d like to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Thanks for your suggestions in advance. Sincerely, Shima -- 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] g_WHAM
Hi, Would you please let me know if it is possible to get just the first 2 histograms of total 24 histograms by running g_WHAM? I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling simulations and not the all. I ran such dat file, but doesn't work and gives me an error of no input file. g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal Thanks in advance. Sincerely, Shima -- 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
Fw: [gmx-users] Umbrella Sampling _ pulled ion
Thanks for your previous replies. All are always beneficial and I appreciate you. As I see in pullx.xvg file, the third column refers to the distance of pull group and reference group. All around -1.2. Is it sufficient to judge that the US has been performed properly? Thanks for your suggestions in advance. Sincerely, Shima - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, July 25, 2013 4:25 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/25/13 7:52 AM, Shima Arasteh wrote: After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I found the F value around 100 kJ/mol/ns. But force constant which I had set in md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has not done properly? Force and force constant are different. The values in the pullf.xvg file indicate the magnitude of force required to maintain the position of the restrained ion. The pullx.xvg will probably be more useful in directly determining how effective the restraining potential was. -Justin ;define = -DPOSRES integrator = md ; leap-frog integrator nsteps =10 ; 1 * 10 = 100 ps dt = 0.001 ; 1 fs nstcomm = 10 tinit = 0 ; Output control nstxout = 5000 ; save coordinates every 100 ps nstvout = 5000 ; save velocities every 100 ps nstenergy = 1000 ; save energies every 2 ps nstfout = 5000 nstxtcout = 5000 ; every 10 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = POPC pull_group1 = Ces_ion pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0.0 0.0 0.00 pull_vec1 = 0 0 1 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution refcoord_scaling = com Would you please let me know your suggestions ? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Wednesday, July 24, 2013 9:41 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:53 AM, Shima Arasteh wrote: Yes, Thanks. Would you give me a hint on this fact that how I would be sure that I am running a correct US ? with proper settings? Either the restraint distance is maintained with acceptable sampling around that distance (given the force constant) or it's not. To save time, I' d prefer to run the US.mdp just for one window. Do you agree with me that if I run an incorrect US for any of the windows, I would get an odd result for npt_US or md_US? It should be pretty easy to see. -Justin Many many thanks for your time and suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
Re: [gmx-users] Umbrella Sampling _ pulled ion
After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I found the F value around 100 kJ/mol/ns. But force constant which I had set in md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has not done properly? ;define = -DPOSRES integrator = md ; leap-frog integrator nsteps =10 ; 1 * 10 = 100 ps dt = 0.001 ; 1 fs nstcomm = 10 tinit = 0 ; Output control nstxout = 5000 ; save coordinates every 100 ps nstvout = 5000 ; save velocities every 100 ps nstenergy = 1000 ; save energies every 2 ps nstfout = 5000 nstxtcout = 5000 ; every 10 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = POPC pull_group1 = Ces_ion pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0.0 0.0 0.00 pull_vec1 = 0 0 1 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution refcoord_scaling = com Would you please let me know your suggestions ? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Sent: Wednesday, July 24, 2013 9:41 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:53 AM, Shima Arasteh wrote: Yes, Thanks. Would you give me a hint on this fact that how I would be sure that I am running a correct US ? with proper settings? Either the restraint distance is maintained with acceptable sampling around that distance (given the force constant) or it's not. To save time, I' d prefer to run the US.mdp just for one window. Do you agree with me that if I run an incorrect US for any of the windows, I would get an odd result for npt_US or md_US? It should be pretty easy to see. -Justin Many many thanks for your time and suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, July 24, 2013 8:05 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:30 AM, Shima Arasteh wrote: Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane. In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file: pull_group1 = Ces_ion So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) : [ system] ... [protein] ... [protein-H] ... [ Ces_ion ] 85563 But after running the grompp, I get this fatal error: File input/output error: index_US.ndx Would you please let
[gmx-users] Umbrella Sampling _ pulled ion
Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane. In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file: pull_group1 = Ces_ion So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) : [ system] ... [protein] ... [protein-H] ... [ Ces_ion ] 85563 But after running the grompp, I get this fatal error: File input/output error: index_US.ndx Would you please let me know how I would be able to define a new group for a specific ion ? Did I make a mistake in defining a new group? Would you please give me any suggestions? Thanks in advance, Sincerely, Shima -- 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] Umbrella Sampling _ pulled ion
Yes, Thanks. Would you give me a hint on this fact that how I would be sure that I am running a correct US ? with proper settings? To save time, I' d prefer to run the US.mdp just for one window. Do you agree with me that if I run an incorrect US for any of the windows, I would get an odd result for npt_US or md_US? Many many thanks for your time and suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, July 24, 2013 8:05 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:30 AM, Shima Arasteh wrote: Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane. In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file: pull_group1 = Ces_ion So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) : [ system] ... [protein] ... [protein-H] ... [ Ces_ion ] 85563 But after running the grompp, I get this fatal error: File input/output error: index_US.ndx Would you please let me know how I would be able to define a new group for a specific ion ? Did I make a mistake in defining a new group? What you did in terms of index group content is fine. The error message means that the file called index_US.ndx is not present in the working directory, or it has the wrong permissions. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] make an index file of COM of lipid bilayer
Hi, Would you please let me know how can I make an index file of COM of lipid membrane? I guess the position of the COM of the bilayer, but how it is possible to make an index file of this point? I want to include this index file as the ref_group in Umbrella Sampling. Sincerely, Shima -- 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
Fw: [gmx-users] make an index file of COM of lipid bilayer
Thanks for your reply. But would you please tell me what is known for the pull_group line? I mean are the atom names or resid-s or residue names or know for it? Sincerely, Shima - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, July 16, 2013 3:39 PM Subject: Re: [gmx-users] make an index file of COM of lipid bilayer On 7/16/13 5:30 AM, Shima Arasteh wrote: Hi, Would you please let me know how can I make an index file of COM of lipid membrane? I guess the position of the COM of the bilayer, but how it is possible to make an index file of this point? I want to include this index file as the ref_group in Umbrella Sampling. Index files can't specify positions, only atoms. In this case, you don't even need a special index group - just use the membrane. The pull code uses the COM of the selected group, so if you specify your membrane, mdrun knows to use its COM. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Umbrella Sampling settings
Allright. As I said earlier, my system is a lipid bilayer. A channel is inserted in it and I want to run US on this system. An ion is considered in center of the each window, the reaction coordinate is set to z, so the group which is pulled is an ion, and my ref group would be COM of the protein. But I don't know what statement is supposed to write in mdp settings exactly: ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = COM of protein pull_group1 = ion pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps IN fact, to implement such settings, how I make the US understand to get the COM of protein as the ref group and the proposed ion as the pulled group? Would you please give me any suggestions? Thanks for all your time and consideration. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 1:41 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 5:10 PM, Shima Arasteh wrote: Thanks for your reply. But when I don't understand why these extra lines are needed to set when are not advantageous practically! :-( There's nothing extra. Everything here has a functional purpose. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 4:21 PM, Shima Arasteh wrote: Hi, I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window. Some mdp file settings for running US, as I found in US tutorial are : ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps But I'd like to know which lines are specifically for US? Because in this step, no group is supposed to be pulled but there are some lines written here related to pulling! All of them are related to umbrella sampling. Pulling (steered MD) and umbrella sampling simply use common parts of the pull code in Gromacs because US requires a restraint potential. Whether or not that restraint potential induces net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate, restrain to a given set of conditions) is the only difference. Both processes require reference and pull groups, geometry information, etc. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] Umbrella Sampling settings
Allright. As I said earlier, my system is a lipid bilayer. A channel is inserted in it and I want to run US on this system. An ion is considered in center of the each window, the reaction coordinate is set to z, so the group which is pulled is an ion, and my ref group would be COM of the protein. But I don't know what statement is supposed to write in mdp settings exactly: ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = COM of protein pull_group1 = ion pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps IN fact, to implement such settings, how I make the US understand to get the COM of protein as the ref group and the proposed ion as the pulled group? Would you please give me any suggestions? Thanks for all your time and consideration. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 1:41 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 5:10 PM, Shima Arasteh wrote: Thanks for your reply. But when I don't understand why these extra lines are needed to set when are not advantageous practically! :-( There's nothing extra. Everything here has a functional purpose. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 4:21 PM, Shima Arasteh wrote: Hi, I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window. Some mdp file settings for running US, as I found in US tutorial are : ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps But I'd like to know which lines are specifically for US? Because in this step, no group is supposed to be pulled but there are some lines written here related to pulling! All of them are related to umbrella sampling. Pulling (steered MD) and umbrella sampling simply use common parts of the pull code in Gromacs because US requires a restraint potential. Whether or not that restraint potential induces net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate, restrain to a given set of conditions) is the only difference. Both processes require reference and pull groups, geometry information, etc. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] Umbrella Sampling settings
Yes, I got Thomas response and I am so grateful in this about. :-) Also many many thanks for your response Justin. Although I don't know the definition of pull-vec yet and I need to study in this about, Would you please let me know if the grompp knows what I wrote as the COM of protein or not? And if it recognizes which ion I mean to be pulled among many ions exist in the whole system? How is it? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 8:16 PM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/12/13 11:32 AM, Shima Arasteh wrote: Allright. As I said earlier, my system is a lipid bilayer. A channel is inserted in it and I want to run US on this system. An ion is considered in center of the each window, the reaction coordinate is set to z, so the group which is pulled is an ion, and my ref group would be COM of the protein. But I don't know what statement is supposed to write in mdp settings exactly: ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = COM of protein pull_group1 = ion pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps IN fact, to implement such settings, how I make the US understand to get the COM of protein as the ref group and the proposed ion as the pulled group? Would you please give me any suggestions? You got a very thorough response already today: http://lists.gromacs.org/pipermail/gmx-users/2013-July/082855.html I see that your settings are now different, using position geometry instead of distance, which is good because that's a better approach for your system. What you haven't specified is pull_vec1, which is necessary when using position geometry. All of these details are discussed to some extent in my umbrella sampling tutorial; it should certainly serve as a basic guide. What you're trying to do is ultimately going to require a slightly different approach, but the general principles and explanations of .mdp terms are the same. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Re: Umbrella Sampling settings
Thanks for your replies. :-) So, if I want to the ion move in only z-direction, I need to set the 'pull_dim' Y Y N? Correct? But in tutorial Justin writes : pull_dim = N N Y: we are pulling only in the z-dimension. Thus, x and y are set to no (N) and z is set to yes (Y). So what should I do?! Sincerely, Shima - Original Message - From: Thomas Schlesier schl...@uni-mainz.de To: gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 9:04 PM Subject: [gmx-users] Re: Umbrella Sampling settings In GROMACS groups are called via the *.ndx file (default: index.ndx) Be aware that 'pull_dim' determines in which diretions (x,y,z) the umbrella potential acts. So use N N Y , if you want that the ion can move freely (onsidering the pull) in the xy-plane and Y Y Y if you want to also restrit the movement in the xy-plane. Am 12.07.2013 17:32, schrieb gmx-users-requ...@gromacs.org: Allright. As I said earlier, my system is a lipid bilayer. A channel is inserted in it and I want to run US on this system. An ion is considered in center of the each window, the reaction coordinate is set to z,? so the group which is pulled is an ion, and my ref group would be COM of the protein. But I don't know what statement is supposed to write in mdp settings exactly: ; Pull code pull??? = umbrella pull_geometry?? = position pull_dim??? = N N Y pull_start? = yes pull_ngroups??? = 1 pull_group0 = COM of protein pull_group1 = ion pull_init1? = 0 pull_rate1? = 0.0 pull_k1 = 4000? ; kJ mol^-1 nm^-2 pull_nstxout??? = 1000? ; every 2 ps pull_nstfout??? = 1000? ; every 2 ps IN fact, to implement such settings, how I make the US understand to get the COM of protein as the ref group and the proposed ion as the pulled group? Would you please give me any suggestions? Thanks for all your time and consideration. Sincerely, Shima - Original Message - From: Justin Lemkuljalem...@vt.edu To: Discussion list for GROMACS usersgmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 1:41 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 5:10 PM, Shima Arasteh wrote: Thanks for your reply. But when I don't understand why these extra lines are needed to set when are not advantageous practically!:-( There's nothing extra.? Everything here has a functional purpose. -Justin Sincerely, Shima - Original Message - From: Justin Lemkuljalem...@vt.edu To: Shima Arastehshima_arasteh2...@yahoo.com; Discussion list for GROMACS usersgmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 4:21 PM, Shima Arasteh wrote: Hi, I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window. Some mdp file settings for running US, as I found in US tutorial are : ; Pull code pull? ? ? ? ? ? = umbrella pull_geometry?? = distance pull_dim? ? ? ? = N N Y pull_start? ? ? = yes pull_ngroups? ? = 1 pull_group0? ?? = Chain_B pull_group1? ?? = Chain_A pull_init1? ? ? = 0 pull_rate1? ? ? = 0.0 pull_k1? ? ? ?? = 4000? ? ? ; kJ mol^-1 nm^-2 pull_nstxout? ? = 1000? ? ? ; every 2 ps pull_nstfout? ? = 1000? ? ? ; every 2 ps But I'd like to know which lines are specifically for US? Because in this step, no group is supposed to be pulled but there are some lines written here related to pulling! All of them are related to umbrella sampling.? Pulling (steered MD) and umbrella sampling simply use common parts of the pull code in Gromacs because US requires a restraint potential.? Whether or not that restraint potential induces net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate, restrain to a given set of conditions) is the only difference.? Both processes require reference and pull groups, geometry information, etc. -Justin -- 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 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] Cyclohexane as a solvent
Dear all, I see cyclohexane parameters in top par CGenFF files. Would it be correct if I add this molecule to the rtp file in charmm and then use it as a solvent rather than for example water? Generally, how is it possible to add a new solvent to the charmm ff simulations? Thanks in advance, Sincerely, Shima -- 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] Umbrella Sampling settings
Hi, I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window. Some mdp file settings for running US, as I found in US tutorial are : ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps But I'd like to know which lines are specifically for US? Because in this step, no group is supposed to be pulled but there are some lines written here related to pulling! Would you please help me in this about? Thanks in advance for your suggestions. Sincerely, Shima -- 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] Umbrella Sampling settings
Thanks for your reply. But when I don't understand why these extra lines are needed to set when are not advantageous practically! :-( Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, July 12, 2013 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 4:21 PM, Shima Arasteh wrote: Hi, I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window. Some mdp file settings for running US, as I found in US tutorial are : ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps But I'd like to know which lines are specifically for US? Because in this step, no group is supposed to be pulled but there are some lines written here related to pulling! All of them are related to umbrella sampling. Pulling (steered MD) and umbrella sampling simply use common parts of the pull code in Gromacs because US requires a restraint potential. Whether or not that restraint potential induces net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate, restrain to a given set of conditions) is the only difference. Both processes require reference and pull groups, geometry information, etc. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Get some specific frames of traj
I tried the tpr file for -s, but doesn't make difference. g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.01 of (3.6, 3.6, 6.3)' -seltype res_com -selrpos res_com -os Would you please give me suggestions? I found some resemble commands in mailing list but didn't find the problem with my command. Thanks in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, July 8, 2013 9:14 PM Subject: Re: [gmx-users] Get some specific frames of traj On 7/8/13 7:50 AM, Shima Arasteh wrote: Thanks for your earlier suggestions. I used the command g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.1 of (36.0, 36.0, 63.0)' -seltype res_com -selrpos res_com -os to find water molecule around a specified coordinate. But I get this error: Input error or input inconsistency: selection(s) could not be parsed Would you please help me with this command? I have not yet tried g_select command. g_select -select 'help all' provides a huge amount of information. Have you tried passing a .tpr file to -s instead? Are your units right? It would seem your box is very big. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 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] pdb files from trajectory
Dear gmx users, I' d like to get pdb files from trajectory, then used the trjconv, # trjconv -f trajout.xtc -o out.pdb -sep It gives fatal error as this: Can not open file: topol.tpr Sincerely, Shima -- 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] Get some specific frames of traj
Dear gmx users, I have a 10 ns simulation trajectory, and like to get some particular frames of it. In fact I want to find the frames in which a specified coordinate is filled with a water molecule, and then pick that frame as an initial structure for the next steps. Is there any script implemented in GROMACS tools or any advantageous tool in this approach? Thanks in advance for your suggestions. Sincerely, Shima -- 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] D-aminoacids in input file
Dear gmx users, I have D amino acids in my input .pdb file. The force field which I aim to use, is CHARMM. I am wondering if I need to modify aminoacids.rtp file? Or it would be OK if I use the same parameters as L aminoacids for D aminoacids? Thanks for your suggestions. They would be appreciated. Sincerely, Shima -- 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] InflateGRO methodology deletion radius
Do you mean another published paper rather than published one in Methods Journal? Another one which explains the algorithm? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 19, 2013 3:45 PM Subject: Re: [gmx-users] InflateGRO methodology deletion radius On 6/19/13 12:39 AM, Shima Arasteh wrote: Do you mean the commands of inflateGRO controls the deletion radius? Yes, that's its purpose. There is a published paper about its algorithm; I would suggest you read and understand it. The command which I use is what I got from tutorial: #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat Am I supposed to decrease 5 as deletion radius? The value of 5 is a grid spacing for the InflateGRO APL measurement. The deletion radius is zero, which is correct for shrinking because you don't want to continue deleting lipids, or you will have no membrane left! Would you please give me a hint to go on? If these concepts are not intuitive, you should absolutely stop and read the paper for InflateGRO and watch the demonstration video that is posted online. -Justin Thanks for your suggestions in advance. Those are really kind of you. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, June 15, 2013 4:18 PM Subject: Re: [gmx-users] InflateGRO methodology deletion radius On 6/15/13 3:56 AM, Shima Arasteh wrote: Hi, In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the lipids, I need to follow the iteration while the cutoff value changed to 0. I' d like to know what settings of EM.mdp file are suggested to get the best results of doing shrinking steps? When I set the settings as follow, the lipids interfere the peptide however the APL doesn't get the experimental value. So the configuration is not ideal to get through the equilibrium steps. define = -DPOSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force 100.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 0.4 ; Cut-off for making neighbor list (short range forces) rlistlong = 6.0 coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 0.4 ; Short-range electrostatic cut-off rvdw = 0.4 ; Short-range Van der Waals cut-off vdwtype = switch rvdw_switch = 0.2 pbc = xyz ; Periodic Boundary Conditions Now, I am wondering if such a settings will serve a proper deletion radius? No. These settings make no sense to me whatsoever. Don't be confused by the cutoff used by InflateGRO and the cutoff values used in the .mdp file. InflateGRO uses a search radius to delete lipids, which is specified on the command line. The cutoff values for the EM and MD runs are dictated by the force field you are using and are in no way connected to lipid deletion. -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 -- 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 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 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
Re: [gmx-users] InflateGRO methodology deletion radius
Do you mean the commands of inflateGRO controls the deletion radius? The command which I use is what I got from tutorial: #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat Am I supposed to decrease 5 as deletion radius? Would you please give me a hint to go on? Thanks for your suggestions in advance. Those are really kind of you. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, June 15, 2013 4:18 PM Subject: Re: [gmx-users] InflateGRO methodology deletion radius On 6/15/13 3:56 AM, Shima Arasteh wrote: Hi, In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the lipids, I need to follow the iteration while the cutoff value changed to 0. I' d like to know what settings of EM.mdp file are suggested to get the best results of doing shrinking steps? When I set the settings as follow, the lipids interfere the peptide however the APL doesn't get the experimental value. So the configuration is not ideal to get through the equilibrium steps. define = -DPOSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force 100.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 0.4 ; Cut-off for making neighbor list (short range forces) rlistlong = 6.0 coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 0.4 ; Short-range electrostatic cut-off rvdw = 0.4 ; Short-range Van der Waals cut-off vdwtype = switch rvdw_switch = 0.2 pbc = xyz ; Periodic Boundary Conditions Now, I am wondering if such a settings will serve a proper deletion radius? No. These settings make no sense to me whatsoever. Don't be confused by the cutoff used by InflateGRO and the cutoff values used in the .mdp file. InflateGRO uses a search radius to delete lipids, which is specified on the command line. The cutoff values for the EM and MD runs are dictated by the force field you are using and are in no way connected to lipid deletion. -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] InflateGRO methodology deletion radius
Hi, In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the lipids, I need to follow the iteration while the cutoff value changed to 0. I' d like to know what settings of EM.mdp file are suggested to get the best results of doing shrinking steps? When I set the settings as follow, the lipids interfere the peptide however the APL doesn't get the experimental value. So the configuration is not ideal to get through the equilibrium steps. define = -DPOSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force 100.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 0.4 ; Cut-off for making neighbor list (short range forces) rlistlong = 6.0 coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 0.4 ; Short-range electrostatic cut-off rvdw = 0.4 ; Short-range Van der Waals cut-off vdwtype = switch rvdw_switch = 0.2 pbc = xyz ; Periodic Boundary Conditions Now, I am wondering if such a settings will serve a proper deletion radius? Sincerely, Shima -- 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] restraints on water oxygen atoms
These are the all commands to do iteration: After generating topology - concatenate the protein and bilayer structure files: #cat dimer-newbox.gro popc-whole.gro system.gro ( Remove unnecessary lines and update the second line of the coordinate file (total number of atoms) accordingly ) - Use a very strong position-restraining force on protein heavy atoms to ensure that the position of the protein does not change during EM : Adding these lines to topology file: ; Strong position restraints for InflateGRO #include topol_Protein_A.itp #ifdef POSRE #include strong_posre.itp #endif #include topol_Protein_B.itp #ifdef POSRE #include strong_posre.itp #endif - Now, generate this new position restraint file using genrestr: #genrestr -f dimer-newbox.gro -o strong_posre.itp -fc 10 10 10 - In the .mdp file used for the minimizations, add a line define = -DSTRONG_POSRES to make use of these new position restraints. - Scale the lipid positions by a factor of 4: #perl inflategro.pl system.gro 6 POPC 14 system_inflated.gro 5 area.dat Updating the .top file and adding POPC 238 to it. ITERATION 1. Energy minimization with restrained protein #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr #mdrun -deffnm em Steepest Descents converged to Fmax 1000 in 137 steps Steepest Descents converged to Fmax 100 in 4998 steps Potential Energy = 1.1410846e+04 Maximum force = 9.4570084e+01 on atom 8800 Norm of force = 3.2672191e+00 scale down the lipids by a factor of 0.95 #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat 2. #grompp -f minim.mdp -c em_shrink1.gro -p topol.top -o em_shrink1.tpr # perl inflategro.pl em_shrink1.gro 0.95 POPC 0 em_shrink2.gro 5 area_shrink2.dat 3. # grompp -f minim.mdp -c em_shrink2.gro -p topol.top -o em_shrink2.tpr # perl inflategro.pl em_shrink2.gro 0.95 POPC 0 em_shrink3.gro 5 area_shrink3.dat . . . . Then, after 32 iterations, the APL reaches the value of 10% higher than the experimental value. So, I use the last gro file em_shrink32.gro as the initial configuration to solvate and next steps. But when I check the overlaps in em_shrink32.gro, there are many improper overlaps and acyl penetration to the protein, disgusting! Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, June 10, 2013 11:12 PM Subject: Re: [gmx-users] restraints on water oxygen atoms On 6/10/13 12:24 PM, Shima Arasteh wrote: Would you please tell me which initial deletion radius? It would be easier for you to provide the exact command(s) you're using. Maybe you've posted this information before, but this thread (or at least, related topics) has gone on for a very long time and maybe I'm forgetting. And do you mean a smaller scale up factor ( for example 0.90 ) by saying shrink more slowly? A larger shrinking factor, e.g. 0.95 or 0.97, will shrink more slowly. -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 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 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] restraints on water oxygen atoms
I put the output file of shrinking steps after 32 iterations: https://jumpshare.com/b/5Y6WUGv7OT1sOFzsrWgN Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, June 11, 2013 3:25 PM Subject: Re: [gmx-users] restraints on water oxygen atoms On 6/11/13 2:05 AM, Shima Arasteh wrote: These are the all commands to do iteration: After generating topology - concatenate the protein and bilayer structure files: #cat dimer-newbox.gro popc-whole.gro system.gro ( Remove unnecessary lines and update the second line of the coordinate file (total number of atoms) accordingly ) - Use a very strong position-restraining force on protein heavy atoms to ensure that the position of the protein does not change during EM : Adding these lines to topology file: ; Strong position restraints for InflateGRO #include topol_Protein_A.itp #ifdef POSRE #include strong_posre.itp #endif #include topol_Protein_B.itp #ifdef POSRE #include strong_posre.itp #endif - Now, generate this new position restraint file using genrestr: #genrestr -f dimer-newbox.gro -o strong_posre.itp -fc 10 10 10 - In the .mdp file used for the minimizations, add a line define = -DSTRONG_POSRES to make use of these new position restraints. - Scale the lipid positions by a factor of 4: #perl inflategro.pl system.gro 6 POPC 14 system_inflated.gro 5 area.dat Updating the .top file and adding POPC 238 to it. ITERATION 1. Energy minimization with restrained protein #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr #mdrun -deffnm em Steepest Descents converged to Fmax 1000 in 137 steps Steepest Descents converged to Fmax 100 in 4998 steps Potential Energy = 1.1410846e+04 Maximum force = 9.4570084e+01 on atom 8800 Norm of force = 3.2672191e+00 scale down the lipids by a factor of 0.95 #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat 2. #grompp -f minim.mdp -c em_shrink1.gro -p topol.top -o em_shrink1.tpr # perl inflategro.pl em_shrink1.gro 0.95 POPC 0 em_shrink2.gro 5 area_shrink2.dat 3. # grompp -f minim.mdp -c em_shrink2.gro -p topol.top -o em_shrink2.tpr # perl inflategro.pl em_shrink2.gro 0.95 POPC 0 em_shrink3.gro 5 area_shrink3.dat . . . . Then, after 32 iterations, the APL reaches the value of 10% higher than the experimental value. So, I use the last gro file em_shrink32.gro as the initial configuration to solvate and next steps. But when I check the overlaps in em_shrink32.gro, there are many improper overlaps and acyl penetration to the protein, disgusting! Please provide a link to an image or images that illustrate what's going on. If molecules are truly overlapping this badly, it sounds like something is very wrong with the force field, since such interactions normally cannot arise without the system blowing up. -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
Re: [gmx-users] restraints on water oxygen atoms
Thanks for your reply. The system I am trying to equilibrate is composed of popc/ peptide/ions/water. I built the system by InflateGRO methodology as you wrote in kalp-dppc tutorial. The last gro file which gave me the acceptable APL, was used as the starting configuration in next steps. But before going on, I found some overlaps between lipids acyl chains and peptide structure. So tried to move the lipid residues caused the overlaps. Then there are some gaps between peptide and near lipid chains. As a result, I see the water cleavage in these regions. Would you please give me any suggestions? How would I make a better packed system without disturbing overlaps or crashes? Would you please help me? Thanks for your suggestions and help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, June 5, 2013 9:25 PM Subject: Re: [gmx-users] restraints on water oxygen atoms On 6/4/13 11:47 PM, Shima Arasteh wrote: Dear gmx users, I have a POPC/peptide/water/ions system. I ran NVT and then NPT on my system. I'd prefer to run the equilibrium steps with position restraints on water oxygen atoms, because the water molecules penetrate the lipid bilayer when running the equilibrium and I don't want it to happen. I tried the NVT with position restraints on water by adding -DPOSRES_WATER to nvt.mdp file and editing the top file by changing the fc to 10. #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 10 10 10 #endif This edition turned into a better result. Now I tried to put such a restraint on npt but the gromacs does not allow it by turning a fatal error: A charge group moved too far between two domain decomposition steps. npt.mdp file: ;NPT equlibration Dimer-POPC-Water - CHARMM36 define = -DPOSRES_LIPID -DPOSRES -DPOSRES_WATER ; P headgroups of POPC and Protein is position restrained (uses the posres.itp file information) integrator = md ; leap-frog integrator nsteps =100 ; 1 * 100 = 1000 ps dt = 0.001 ; 1 fs ; Output control nstxout = 2000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 1000 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K pcoupl = Berendsen ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 310 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = Protein_POPC Water_Ces_CL refcoord_scaling = com I am wondering how it is possible to prevent penetrating the water molecules through equilibrium? And how I can put the restraint in npt as well as nvt? Would you please help me in this issue please? Restraints in all directions, especially with pressure coupling, will undoubtedly lead to nasty atomic clashes and the failure that you're seeing. Normally, one does not need to apply restraints in any other dimension aside from z, to prevent vertical diffusion
Re: [gmx-users] restraints on water oxygen atoms
Thanks for your reply. When I look into the earlier gro file ( with APL even higher than 10% of desired APL), I still see some lipid residues in improper places, forexample in phenyl rings. How can I go on with it? If I choose the gro file without any overlap, the APL becomes very high and it would not be acceptable. Do you still suggest not to delete lipids manually? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, June 10, 2013 4:50 PM Subject: Re: [gmx-users] restraints on water oxygen atoms On 6/10/13 3:37 AM, Shima Arasteh wrote: Thanks for your reply. The system I am trying to equilibrate is composed of popc/ peptide/ions/water. I built the system by InflateGRO methodology as you wrote in kalp-dppc tutorial. The last gro file which gave me the acceptable APL, was used as the starting configuration in next steps. But before going on, I found some overlaps between lipids acyl chains and peptide structure. So tried to move the lipid residues caused the overlaps. Then there are some gaps between peptide and near lipid chains. As a result, I see the water cleavage in these regions. Would you please give me any suggestions? How would I make a better packed system without disturbing overlaps or crashes? Would you please help me? Don't manually delete lipids. InflateGRO overestimates APL, so if you reach your target value, realize that the lipids are more packed than that and the true APL is much smaller. I discuss that fact in the KALP-DPPC tutorial. I generally stop packing when the lipids claim to be about 10% higher than the desired APL. If you delete lipids because you've forced them together too much, then you're going to severely compromise the membrane. -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 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 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] restraints on water oxygen atoms
Would you please tell me which initial deletion radius? And do you mean a smaller scale up factor ( for example 0.90 ) by saying shrink more slowly? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, June 10, 2013 8:22 PM Subject: Re: [gmx-users] restraints on water oxygen atoms On 6/10/13 11:44 AM, Shima Arasteh wrote: Thanks for your reply. When I look into the earlier gro file ( with APL even higher than 10% of desired APL), I still see some lipid residues in improper places, forexample in phenyl rings. How can I go on with it? If I choose the gro file without any overlap, the APL becomes very high and it would not be acceptable. Do you still suggest not to delete lipids manually? I don't see how that's possible, quite honestly. If the initial deletion radius was sufficient, then lipid molecules shouldn't force their way through phenyl rings - the forces required would be astronomical. I don't have any details of your protocol, so it's hard to comment further. If things are getting jammed together this badly, you should probably be shrinking more slowly than you currently are. I never advocate for manual deletion of lipids, because, as you can see from experience, doing so creates a world of problems during equilibration. -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] restraints on water oxygen atoms
Dear gmx users, I have a POPC/peptide/water/ions system. I ran NVT and then NPT on my system. I'd prefer to run the equilibrium steps with position restraints on water oxygen atoms, because the water molecules penetrate the lipid bilayer when running the equilibrium and I don't want it to happen. I tried the NVT with position restraints on water by adding -DPOSRES_WATER to nvt.mdp file and editing the top file by changing the fc to 10. #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 10 10 10 #endif This edition turned into a better result. Now I tried to put such a restraint on npt but the gromacs does not allow it by turning a fatal error: A charge group moved too far between two domain decomposition steps. npt.mdp file: ;NPT equlibration Dimer-POPC-Water - CHARMM36 define = -DPOSRES_LIPID -DPOSRES -DPOSRES_WATER ; P headgroups of POPC and Protein is position restrained (uses the posres.itp file information) integrator = md ; leap-frog integrator nsteps =100 ; 1 * 100 = 1000 ps dt = 0.001 ; 1 fs ; Output control nstxout = 2000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 1000 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K pcoupl = Berendsen ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 310 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = Protein_POPC Water_Ces_CL refcoord_scaling = com I am wondering how it is possible to prevent penetrating the water molecules through equilibrium? And how I can put the restraint in npt as well as nvt? Would you please help me in this issue please? Sincerely, Shima -- 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] water position restraints
Dear GMX users, I' d like to put the position restraints on water oxygen atoms. To do so, I made a water_posre.itp file. Then I modified the top file, as this, but didn't work: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #include water_posre.itp #endif Would you please help me here? I don't know how I change the fcx, fcy, and fcz. Is it possible to change the fc values 1000 to 10 in top file by just text editing as below: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 10 10 10 #include water_posre.itp #endif Sincerely, Shima -- 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] water position restraints
I just applied genrestr command: #genrestr -f minim.gro -o water_posre.itp -fc 10 10 10 And then I just chose the water to create the water_posre.itp. Would not that work? Sincerely, Shima From: Mark Abraham mark.j.abra...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, June 2, 2013 3:35 PM Subject: Re: [gmx-users] water position restraints What's in that .itp? You can only restrain all the waters that have that moleculetype. See http://www.gromacs.org/Documentation/How-tos/Position_Restraints On Sun, Jun 2, 2013 at 9:52 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear GMX users, I' d like to put the position restraints on water oxygen atoms. To do so, I made a water_posre.itp file. Then I modified the top file, as this, but didn't work: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #include water_posre.itp #endif Would you please help me here? I don't know how I change the fcx, fcy, and fcz. Is it possible to change the fc values 1000 to 10 in top file by just text editing as below: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 10 10 10 #include water_posre.itp #endif Sincerely, Shima -- 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 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] Add CS ions to system
Hi all, I want to add CS ions to my system by genion but it seems impossible when go through the EM. The molecule section in my top file is: Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 20406 NA 681 CL 702 CS 19 The commands to neutralize and adding CsCl are as follow: Adding ions: #grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr #genion -s ions.tpr -o system_solv_ions.gro -p topol.top -conc 1 -neutral Adding 19 pairs of CsCl: #grompp -f ions.mdp -c system_solv_ions.gro -p topol.top -o ions_CsCl.tpr #genion -s ions_CsCl.tpr -o system_solv_ions_CsCl.gro -p topol.top -pname CS -np 19 -nname CL -nn 19 EM: And fatal error as I get is: #grompp -f minim.mdp -c system_solv_ions_CsCl.gro -p topol.top -o minim.tpr Fatal error: No such moleculetype CS But I see the CS ion in residuetypes.dat which exist in my directory : CS Ion So what's the reason? If it is related to the version of applied GROMACS? I am working with 4.5.5 GROMACS and CHARMM 36 FF. Thanks. Would you give me any suggestions? Sincerely, Shima -- 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] puuling simulations
http://www.gromacs.org/Documentation/Tutorials Sincerely, Shima - Original Message - From: Sathish Kumar sathishk...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 2:08 PM Subject: [gmx-users] puuling simulations Sir, I want to do pulling simulations for membrane protein and gold nanoparticles. Can you please suggest me some tutorials. Thank You -- regards M.SathishKumar -- 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 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] Re: Running Pull Code
Thanks for your reply. It' s around 5 nano seconds that I ran equilibration time on the system, and the average pressure I see as a result, seems sensible. However I am not sure if this criteria is sufficient? Others suggest to evaluate the box-dimension changes using g_energy code to judge of sufficient equilibration time. I appreciate your suggestion. Sincerely, Shima - Original Message - From: Thomas Schlesier schl...@uni-mainz.de To: gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 3:30 PM Subject: [gmx-users] Re: Running Pull Code The three steps (EM, NVT and NPT) are to equilibrate the system. How much time these steps need depends on the system. But i would assume a ouple of nanosecounds are sufficient for most systems. You could look into the literature, how long other people equilibrate systems which are similar to ours. If the system is equilibrated, you an start to perform the pulling simulation to obtain the individual structure for the later umbrella sampling. Greetings Thomas Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: Hi, I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling. I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT? As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well? Would you please give me any suggestions? Thanks in advance. Sincerely, Shima? -- 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 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] Re: Running Pull Code
Thanks for your reply. In fact, I plan to study ion conduction through the peptide inserted in lipid membrane and acting as an ion channel. According to the literature, an ion across the membrane in less than 20 ns. Can I decide upon this information to apply pull code? You simulated the protofibril structures for 100 ns, in another article 25 ns. Ok, if there is not any universal recipe for it, what do you suggest me? Try and error? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 4:02 PM Subject: Re: [gmx-users] Re: Running Pull Code On 5/17/13 7:16 AM, Shima Arasteh wrote: Thanks for your reply. It' s around 5 nano seconds that I ran equilibration time on the system, and the average pressure I see as a result, seems sensible. However I am not sure if this criteria is sufficient? Others suggest to evaluate the box-dimension changes using g_energy code to judge of sufficient equilibration time. The box vectors won't tell you anything more than the pressure will since they're related quantities. The better question is, What is a suitable starting structure for the system of interest? The umbrella sampling tutorial (which everyone seems to take at literal face value as the only way to do things, which it is decidedly not) presents a simple, easy-to-understand method. In the paper I did (upon which I based the tutorial), I simulated the protofibril structures for 100 ns before I was confident they were suitably stable and representative of viable structures for doing SMD and US. Your mileage will vary and depends on the quality of the starting structure and what it is that you hope to determine. There is no magic recipe that is universal. -Justin I appreciate your suggestion. Sincerely, Shima - Original Message - From: Thomas Schlesier schl...@uni-mainz.de To: gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 3:30 PM Subject: [gmx-users] Re: Running Pull Code The three steps (EM, NVT and NPT) are to equilibrate the system. How much time these steps need depends on the system. But i would assume a ouple of nanosecounds are sufficient for most systems. You could look into the literature, how long other people equilibrate systems which are similar to ours. If the system is equilibrated, you an start to perform the pulling simulation to obtain the individual structure for the later umbrella sampling. Greetings Thomas Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: Hi, I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling. I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT? As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well? Would you please give me any suggestions? Thanks in advance. Sincerely, Shima? -- 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
Re: [gmx-users] Re: Running Pull Code
Thanks for your reply. In fact, I plan to study ion conduction through the peptide inserted in lipid membrane and acting as an ion channel. According to the literature, an ion across the membrane in less than 20 ns. Can I decide upon this information to apply pull code? You simulated the protofibril structures for 100 ns, in another article 25 ns. Ok, if there is not any universal recipe for it, what do you suggest me? Try and error? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 4:02 PM Subject: Re: [gmx-users] Re: Running Pull Code On 5/17/13 7:16 AM, Shima Arasteh wrote: Thanks for your reply. It' s around 5 nano seconds that I ran equilibration time on the system, and the average pressure I see as a result, seems sensible. However I am not sure if this criteria is sufficient? Others suggest to evaluate the box-dimension changes using g_energy code to judge of sufficient equilibration time. The box vectors won't tell you anything more than the pressure will since they're related quantities. The better question is, What is a suitable starting structure for the system of interest? The umbrella sampling tutorial (which everyone seems to take at literal face value as the only way to do things, which it is decidedly not) presents a simple, easy-to-understand method. In the paper I did (upon which I based the tutorial), I simulated the protofibril structures for 100 ns before I was confident they were suitably stable and representative of viable structures for doing SMD and US. Your mileage will vary and depends on the quality of the starting structure and what it is that you hope to determine. There is no magic recipe that is universal. -Justin I appreciate your suggestion. Sincerely, Shima - Original Message - From: Thomas Schlesier schl...@uni-mainz.de To: gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 3:30 PM Subject: [gmx-users] Re: Running Pull Code The three steps (EM, NVT and NPT) are to equilibrate the system. How much time these steps need depends on the system. But i would assume a ouple of nanosecounds are sufficient for most systems. You could look into the literature, how long other people equilibrate systems which are similar to ours. If the system is equilibrated, you an start to perform the pulling simulation to obtain the individual structure for the later umbrella sampling. Greetings Thomas Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: Hi, I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling. I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT? As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well? Would you please give me any suggestions? Thanks in advance. Sincerely, Shima? -- 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] visualizing the system
Hi, I am simulating a system composed if POPC , peptide, waters and ions. I used the InflateGRO methodology to construct the system. There are 2 phenylalanine residues in my peptide. Each phenyl has 2rings connected from one side. After inflategro one of the phenyl rings is normal, but the other is not because What I see them in vmd, there are 2rings remain close to eachother but the expected bonds between them are not visible. The top file shows the correct bonds and angles and ... . I ran EM, NVT, NPT, and thought this problem would be solved but it is still as well as before. The EM was also ok and did not show high enegy or crash. Does this problem relate to the vmd and its algorithms? Or there is a problem with my system. How would the rings look usual? How could I solve it? Thanks in advance. Sincerely, Shima -- 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] Tryptophan rings are not connected in visualization
Hi, I am simulating a system composed if POPC , peptide, waters and ions. I used the InflateGRO methodology to construct the system. There are 2 Tryptophan residues in my peptide. Each Tryptophan has 2rings connected from one side. After inflategro one of the Tryptophan rings is normal, but the other is not because What I see them in vmd, there are 2rings remain close to eachother but the expected bonds between them are not visible. The top file shows the correct bonds and angles and ... . I ran EM, NVT, NPT, and thought this problem would be solved but it is still as well as before. The EM was also ok and did not show high enegy or crash. Does this problem relate to the vmd and its algorithms? Or there is a problem with my system. How would the rings look usual? How could I solve it? Thanks in advance. Sincerely, Shima -- 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] Re: Running Pull Code
If I skip the pulling code step, how could I generate configurations while there are one ion in each window? Am I supposed to save my favorite snapshots during MD simulation trajectory? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 4:02 PM Subject: Re: [gmx-users] Re: Running Pull Code On 5/17/13 7:16 AM, Shima Arasteh wrote: Thanks for your reply. It' s around 5 nano seconds that I ran equilibration time on the system, and the average pressure I see as a result, seems sensible. However I am not sure if this criteria is sufficient? Others suggest to evaluate the box-dimension changes using g_energy code to judge of sufficient equilibration time. The box vectors won't tell you anything more than the pressure will since they're related quantities. The better question is, What is a suitable starting structure for the system of interest? The umbrella sampling tutorial (which everyone seems to take at literal face value as the only way to do things, which it is decidedly not) presents a simple, easy-to-understand method. In the paper I did (upon which I based the tutorial), I simulated the protofibril structures for 100 ns before I was confident they were suitably stable and representative of viable structures for doing SMD and US. Your mileage will vary and depends on the quality of the starting structure and what it is that you hope to determine. There is no magic recipe that is universal. -Justin I appreciate your suggestion. Sincerely, Shima - Original Message - From: Thomas Schlesier schl...@uni-mainz.de To: gmx-users@gromacs.org Cc: Sent: Friday, May 17, 2013 3:30 PM Subject: [gmx-users] Re: Running Pull Code The three steps (EM, NVT and NPT) are to equilibrate the system. How much time these steps need depends on the system. But i would assume a ouple of nanosecounds are sufficient for most systems. You could look into the literature, how long other people equilibrate systems which are similar to ours. If the system is equilibrated, you an start to perform the pulling simulation to obtain the individual structure for the later umbrella sampling. Greetings Thomas Am 17.05.2013 07:46, schrieb gmx-users-requ...@gromacs.org: Hi, I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling. I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT? As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well? Would you please give me any suggestions? Thanks in advance. Sincerely, Shima? -- 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] Running Pull Code
Hi, I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling. I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT? As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well? Would you please give me any suggestions? Thanks in advance. Sincerely, Shima -- 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] unstable system
0. 4725 4727 81.0 0.1115 0.1850 0. 4725 4726 72.6 0.1116 0.1915 0. 4722 4725 169.8 0.1585 0.4552 0.1530 4722 4724 116.2 0.1162 0.4645 0. 4722 4723 118.2 0.1150 0.4643 0. 4719 4722 66.4 0.1585 2.2611 0.1530 4719 4721 68.2 0.1118 1.7639 0. 4719 4720 71.0 0.1114 2.1695 0. 4716 4719 111.2 0.1565 2.5385 0.1530 Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 4719 and 4726 at distance 2.217 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size --- Program mdrun, VERSION 4.5.5 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/mdlib/pme.c, line: 538 Fatal error: 2 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. Would you please give me your suggestions? Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Justin Lemkul jalem...@vt.edu; gmx-users@gromacs.org gmx-users@gromacs.org Cc: Sent: Wednesday, May 8, 2013 7:53 PM Subject: Re: [gmx-users] unstable system Yes, all steps were completed successfully. About your tips, OK sir. I' m going to go through the minimization and NVT and NPT again. Lets get my result, then will post the exact commands. Thanks for your suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, May 8, 2013 5:07 PM Subject: Re: [gmx-users] unstable system On 5/8/13 2:35 AM, Shima Arasteh wrote: OK. 1. Exact commands given in the preparation protocol (EM and equilibration) EM: # grompp -f minim.mdp -c input.gro -p topol.top -o minim.tpr #mdrun -deffnm minim NVT: #grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr #mdrun -deffnm nvt -v NPT: # grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr # mdrun_mpi -deffnm npt *** Next removed some disturbing water molecules, so edited topol file and made a new index file index_mod_2.ndx: Ran a new EM: # grompp -f npt.mdp -c npt_mod.gro -p topol.top -o npt_minim.tpr # mdrun -deffnm npt_minim Ran a new NPT: # grompp -f npt.mdp -c npt_minim.gro -p topol.top -n index_mod_2.ndx -o npt.tpr # mdrun_mpi -deffnm npt I repeated the NPT the same as above in 3 steps: a) restraints on lipid phosphorous and protein for 1 ns b) restraints on protein for 1ns c) restraint on protein with less force for 2 ns All 3 of these steps complete successfully? MD: # grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index_mod_2.ndx -o md_0_1.tpr # mdrun -deffnm npt There are a few discrepancies in the commands you have shown here, in particular naming differences between input and output file names. I ask for exact commands (not what you think you remember) for a very important reason - the diagnostic information you have provided (from the .log file) seems to indicate that the previous equilibrated state was not passed along to the MD step, so I suspect you've left out a checkpoint file somewhere or you have regenerated velocities by accident. As a tip, write all of your commands in a shell script and execute the script. Then, if something goes wrong and someone asks for exact commands, just copy and paste. I still can't tell if this is actually what you did. 3 particles communicated to PME node 2 are more than 2/3 times the cut - off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. 2. The .mdp files being used for all steps, most importantly NPT and MD npt.mdp: ;NPT equlibration Dimer-POPC-Water - CHARMM36 define = -DPOSRES integrator = md ; leap-frog integrator nsteps =100 ; 1 * 100 = 1000 ps dt = 0.001 ; 1 fs ; Output control nstxout = 2000 ; save coordinates every 0.4 ps nstvout = 2000 ; save velocities every 0.2 ps nstenergy = 1000 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order
[gmx-users] US and SMD
Hi, In Umbrella Sampling method, among mdp settings, there is a section where the pull code settings are defined in: pull = umbrella: using a harmonic potential to pull As it is said that with US the path of the permeating ion along thereaction coordinate is sampled using many discrete windows, whereas with SMD the ion is pulledalong this same reaction coordinate, I am on a doubt that how the pull code with a harmonic potential works here? I am little confused. Would you please giveme a hint to understand it? Thanks in advance. Your suggestionswould be appreciated . Sincerely, Shima -- 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] unstable system
= switch rvdw_switch = 1.0 ; Parameters for treating bonded interactions continuation = yes ; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 1 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 4 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = Nose-Hoover ; Modified Berendsen thermostat using velocity rescaling tc-grps = Protein_POPC Water_and_ions ; Define groups to be coupled separately to temperature bath tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps) ref_t = 310 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT conditions pcoupltype = semiisotropic ; Isotropic scaling in the x-y direction, independent of the z direction tau_p = 2.0 ; Coupling time constant (ps) ref_p = 1.01325 1.01325 ; Reference pressure for coupling, x-y, z directions (bar) compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility (bar^-1) ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel = no ; Velocity is read from the previous run ; Centre of mass (COM) motion removal relative to the specified groups nstcomm = 1 ; COM removal frequency (steps) comm_mode = Linear ; Remove COM translation (linear / angular / no) comm_grps =Protein_POPC Water_and_ions ; COM removal relative to the specified groups Would you please help me? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, May 8, 2013 2:16 AM Subject: Re: [gmx-users] unstable system On 5/7/13 2:42 PM, Shima Arasteh wrote: Hi, I have run a new npt after energy minimization on my system composed of water/protein/lipid/ions. After a few nanoseconds for NPT, I ran MD, and got fatal error : X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group What is written in md.log file shows an improper pressure, Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 8.26284e+04 5.54129e+04 7.43891e+02 -1.96405e+02 8.37087e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.05973e+05 8.51736e+04 -5.79669e+03 -1.11865e+06 -2.67464e+05 Position Rest. Potential Kinetic En. Total Energy Temperature 2.09408e+03 -1.26366e+06 3.33724e+05 -9.29932e+05 4.44648e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -1.09245e+02 -2.40668e+04 6.65938e-04 I' d like to know if it means that more that the system is required of more npt equilibration? Thanks for your suggestion. Please help me. There is no reason why NPT should run stably but MD would then fail. The high initial temperature suggests that atoms are overlapping somehow or that the previous state has not been preserved properly. Please provide exact details of what you are doing, including the following: 1. Exact commands given in the preparation protocol (EM and equilibration) 2. The .mdp files being used for all steps, most importantly NPT and MD 3. Your grompp and mdrun invocations for the failing MD run -Justin - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 11:29 PM Subject: Re: [gmx-users] unstable system On 4/19/13 2:57 PM, Shima Arasteh wrote: Thanks so much for your replies. I appreciate you. Do you think that more NPT equilibration might solve the problem? or wont work? I have no idea at what point you are in your procedure that is crashing. I'm not going to make some blind assessment of do more NPT or some random
Re: [gmx-users] unstable system
Yes, all steps were completed successfully. About your tips, OK sir. I' m going to go through the minimization and NVT and NPT again. Lets get my result, then will post the exact commands. Thanks for your suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, May 8, 2013 5:07 PM Subject: Re: [gmx-users] unstable system On 5/8/13 2:35 AM, Shima Arasteh wrote: OK. 1. Exact commands given in the preparation protocol (EM and equilibration) EM: # grompp -f minim.mdp -c input.gro -p topol.top -o minim.tpr #mdrun -deffnm minim NVT: #grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr #mdrun -deffnm nvt -v NPT: # grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr # mdrun_mpi -deffnm npt *** Next removed some disturbing water molecules, so edited topol file and made a new index file index_mod_2.ndx: Ran a new EM: # grompp -f npt.mdp -c npt_mod.gro -p topol.top -o npt_minim.tpr # mdrun -deffnm npt_minim Ran a new NPT: # grompp -f npt.mdp -c npt_minim.gro -p topol.top -n index_mod_2.ndx -o npt.tpr # mdrun_mpi -deffnm npt I repeated the NPT the same as above in 3 steps: a) restraints on lipid phosphorous and protein for 1 ns b) restraints on protein for 1ns c) restraint on protein with less force for 2 ns All 3 of these steps complete successfully? MD: # grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index_mod_2.ndx -o md_0_1.tpr # mdrun -deffnm npt There are a few discrepancies in the commands you have shown here, in particular naming differences between input and output file names. I ask for exact commands (not what you think you remember) for a very important reason - the diagnostic information you have provided (from the .log file) seems to indicate that the previous equilibrated state was not passed along to the MD step, so I suspect you've left out a checkpoint file somewhere or you have regenerated velocities by accident. As a tip, write all of your commands in a shell script and execute the script. Then, if something goes wrong and someone asks for exact commands, just copy and paste. I still can't tell if this is actually what you did. 3 particles communicated to PME node 2 are more than 2/3 times the cut - off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. 2. The .mdp files being used for all steps, most importantly NPT and MD npt.mdp: ;NPT equlibration Dimer-POPC-Water - CHARMM36 define = -DPOSRES integrator = md ; leap-frog integrator nsteps =100 ; 1 * 100 = 1000 ps dt = 0.001 ; 1 fs ; Output control nstxout = 2000 ; save coordinates every 0.4 ps nstvout = 2000 ; save velocities every 0.2 ps nstenergy = 1000 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_and_ions ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K pcoupl = Berendsen ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 310 ; temperature for Maxwell distribution ;gen_seed = -1
Re: [gmx-users] unstable system
Hi, I have run a new npt after energy minimization on my system composed of water/protein/lipid/ions. After a few nanoseconds for NPT, I ran MD, and got fatal error : X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group What is written in md.log file shows an improper pressure, Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 8.26284e+04 5.54129e+04 7.43891e+02 -1.96405e+02 8.37087e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.05973e+05 8.51736e+04 -5.79669e+03 -1.11865e+06 -2.67464e+05 Position Rest. Potential Kinetic En. Total Energy Temperature 2.09408e+03 -1.26366e+06 3.33724e+05 -9.29932e+05 4.44648e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -1.09245e+02 -2.40668e+04 6.65938e-04 I' d like to know if it means that more that the system is required of more npt equilibration? Thanks for your suggestion. Please help me. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 11:29 PM Subject: Re: [gmx-users] unstable system On 4/19/13 2:57 PM, Shima Arasteh wrote: Thanks so much for your replies. I appreciate you. Do you think that more NPT equilibration might solve the problem? or wont work? I have no idea at what point you are in your procedure that is crashing. I'm not going to make some blind assessment of do more NPT or some random thing. If you just completed the EM as you posted, proceed with whatever equilibration protocol you believe to be sufficient. There is no one single answer here. If you're jumping straight into MD after the EM you showed, you need to start your equilibration over again completely. -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] RMSD
Hi, I' like to know if it is possible to get the average RMSD through g_rms command? Or I need to get it manually? Thanks for your suggestions. Sincerely, Shima -- 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] umbrella sampling tutorial
Dear Justin, About Umbrella sampling tutorial, would you please let me know why you created an index file contains of chain A and chain B? Also, what's the meaning of 19 and 20 created by a text editoras groups.txt file? I can not understand this. Thanks in advance. Sincerely, Shima -- 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] renumtop script
Hi all, I aimed to use renumtop script, downloaded from other softwares in GROMACS.org website. Does anybody know which language this script is written in? Because I want to execute this program and write a command as follow, but it doesn't work: # renumtop topol.top The error what I get in bash is this: If 'renumtop' is not a typo you can use command-not-found to lookup the package that contains it, like this: cnf renumtop I think some prerequisite software are need to applied but they don't exist. And also don't know what they are to go on installation of them. Would you please let me know how to solve this problem? Thanks for your suggestions. Sincerely, Shima -- 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] renumtop script
Hi all, I aimed to use renumtop script, downloaded from other softwares in GROMACS.org website. Does anybody know which language this script is written in? Because I want to execute this program and write a command as follow, but it doesn't work: # renumtop topol.top The error what I get in bash is this: If 'renumtop' is not a typo you can use command-not-found to lookup the package that contains it, like this: cnf renumtop I think some prerequisite software are need to applied but they don't exist. And also don't know what they are to go on installation of them. Would you please let me know how to solve this problem? Thanks for your suggestions. Sincerely, Shima -- 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] unstable system
Hi, I tried to equilibrate my system by setting timestep=1 fts and decreasing the position restraints step by step. But when I go to MDRUN step, it doesnt work and some pdb files are printed. what is printed in my log file is as follow: Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 8.34161e+04 5.57602e+04 7.65365e+02 -1.97155e+02 8.52248e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.06644e+05 8.46716e+04 -5.77343e+03 -1.11612e+06 -2.67240e+05 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -1.26284e+06 6.13687e+05 -6.49154e+05 8.17667e+02 -1.08370e+02 Pressure (bar) Constr. rmsd -8.62031e+04 5.99322e-04 Would you please give me any suggestions? Does my system need more equilibration yet? longer equilibration time? Whats the problem? My settings as sent you earlier seem fine, so whats the solution? Thanks for your suggestions. They would be appreciated. Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 7, 2013 4:46 PM Subject: Re: [gmx-users] unstable system On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Hi all, I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually. I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group . I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I don't get many pdb files to see. As what I see in Diagnosing unstable system web page, 1. it would be beneficial if one see what part of the system is unstable in first steps. As I saw, the unstable POPC hydrogen atoms are not fine. 2. The single molecules are supposed to examine in water or vacuum too. I have passed this step successfully. 3. I have not ignored any warning during the last steps. 4. And my mdp files to run md is as follow: integrator = md dt = 0.002 nsteps = 500 ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 1.0 What force field are you using? CHARMM? In any case, the value of rvdw_switch does not make any sense. If you're using CHARMM, it should be 1.0. ; Parameters for treating bonded interactions continuation = yes constraint_algorithm = LINCS NCS / SHAKE) constraints = all-bonds ) lincs_iter = 1 lincs_order = 4 ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = Nose-Hoover tc-grps = Protein_POPC Water_and_ions ; Define groups to be coupled separately to temperature bath tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps) ref_t = 310 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Initial Velocity Generation gen_vel = no ; Centre of mass (COM) motion removal relative to the specified groups nstcomm = 1 y (steps) comm_mode = Linear comm_grps =Protein_POPC Water_and_ions ; COM removal relative to the specified groups Would you please let me know if these happen due to an improper equilibration? Do I need to extend the NPT step? Would that fix it? Aside from the above comment, there is nothing particularly wrong about the .mdp file aside from some odd characters here and there, which I will assume are nothing more than quirks of transferring to an email
Re: [gmx-users] unstable system
Thanks for your reply. I' d like to know if I need to remove all position restraints before MDRUN?means that the last step of npt should be done without position restraints? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 7:58 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:26 AM, Shima Arasteh wrote: Hi, I tried to equilibrate my system by setting timestep=1 fts and decreasing the position restraints step by step. But when I go to MDRUN step, it doesnt work and some pdb files are printed. what is printed in my log file is as follow: Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 8.34161e+04 5.57602e+04 7.65365e+02 -1.97155e+02 8.52248e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.06644e+05 8.46716e+04 -5.77343e+03 -1.11612e+06 -2.67240e+05 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -1.26284e+06 6.13687e+05 -6.49154e+05 8.17667e+02 -1.08370e+02 Pressure (bar) Constr. rmsd -8.62031e+04 5.99322e-04 Would you please give me any suggestions? Does my system need more equilibration yet? longer equilibration time? Whats the problem? My settings as sent you earlier seem fine, so whats the solution? Thanks for your suggestions. They would be appreciated. The temperature is 817 K, indicating something is moving with a ridiculously high velocity that has been imparted by strong forces. You have atoms overlapping somewhere. Try more thorough energy minimization. -Justin Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 7, 2013 4:46 PM Subject: Re: [gmx-users] unstable system On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Hi all, I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually. I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group . I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I don't get many pdb files to see. As what I see in Diagnosing unstable system web page, 1. it would be beneficial if one see what part of the system is unstable in first steps. As I saw, the unstable POPC hydrogen atoms are not fine. 2. The single molecules are supposed to examine in water or vacuum too. I have passed this step successfully. 3. I have not ignored any warning during the last steps. 4. And my mdp files to run md is as follow: integrator = md dt = 0.002 nsteps = 500 ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 1.0 What force field are you using? CHARMM? In any case, the value of rvdw_switch does not make any sense. If you're using CHARMM, it should be 1.0. ; Parameters for treating bonded interactions continuation = yes constraint_algorithm = LINCS NCS / SHAKE) constraints = all-bonds ) lincs_iter = 1 lincs_order = 4 ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = Nose-Hoover tc-grps = Protein_POPC Water_and_ions ; Define groups to be coupled separately to temperature bath tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps) ref_t = 310 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres
Re: [gmx-users] unstable system
All right. And if minimization doesnt fix such a problem, what would be the solution? However I have not tried it on my own system yet. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 8:22 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:43 AM, Shima Arasteh wrote: Thanks for your reply. I' d like to know if I need to remove all position restraints before MDRUN?means that the last step of npt should be done without position restraints? Whatever makes sense for your system. There is no universal answer to how equilibration should be done. If your simulation is crashing at step zero, I doubt that removing restraints will help in any way. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 7:58 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:26 AM, Shima Arasteh wrote: Hi, I tried to equilibrate my system by setting timestep=1 fts and decreasing the position restraints step by step. But when I go to MDRUN step, it doesnt work and some pdb files are printed. what is printed in my log file is as follow: Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 8.34161e+04 5.57602e+04 7.65365e+02 -1.97155e+02 8.52248e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.06644e+05 8.46716e+04 -5.77343e+03 -1.11612e+06 -2.67240e+05 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -1.26284e+06 6.13687e+05 -6.49154e+05 8.17667e+02 -1.08370e+02 Pressure (bar) Constr. rmsd -8.62031e+04 5.99322e-04 Would you please give me any suggestions? Does my system need more equilibration yet? longer equilibration time? Whats the problem? My settings as sent you earlier seem fine, so whats the solution? Thanks for your suggestions. They would be appreciated. The temperature is 817 K, indicating something is moving with a ridiculously high velocity that has been imparted by strong forces. You have atoms overlapping somewhere. Try more thorough energy minimization. -Justin Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 7, 2013 4:46 PM Subject: Re: [gmx-users] unstable system On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Hi all, I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually. I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group . I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I don't get many pdb files to see. As what I see in Diagnosing unstable system web page, 1. it would be beneficial if one see what part of the system is unstable in first steps. As I saw, the unstable POPC hydrogen atoms are not fine. 2. The single molecules are supposed to examine in water or vacuum too. I have passed this step successfully. 3. I have not ignored any warning during the last steps. 4. And my mdp files to run md is as follow: integrator = md dt = 0.002 nsteps = 500 ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 1.0 What force field are you using? CHARMM? In any case, the value of rvdw_switch does not make any sense. If you're using CHARMM, it should be 1.0. ; Parameters for treating bonded interactions continuation = yes constraint_algorithm = LINCS NCS / SHAKE) constraints = all-bonds ) lincs_iter = 1 lincs_order = 4 ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation
Re: [gmx-users] unstable system
:-) OK, thanks. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 8:42 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:55 AM, Shima Arasteh wrote: All right. And if minimization doesnt fix such a problem, what would be the solution? However I have not tried it on my own system yet. It's a waste of time to delve into hypotheticals. Please try the advice you've been given and report back if needed. Crashes like you are seeing are almost invariably due to poor starting configuration. Thorough EM solves that problem. If, for some reason, that doesn't work, we will continue to diagnose. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 8:22 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:43 AM, Shima Arasteh wrote: Thanks for your reply. I' d like to know if I need to remove all position restraints before MDRUN?means that the last step of npt should be done without position restraints? Whatever makes sense for your system. There is no universal answer to how equilibration should be done. If your simulation is crashing at step zero, I doubt that removing restraints will help in any way. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 7:58 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:26 AM, Shima Arasteh wrote: Hi, I tried to equilibrate my system by setting timestep=1 fts and decreasing the position restraints step by step. But when I go to MDRUN step, it doesnt work and some pdb files are printed. what is printed in my log file is as follow: Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 8.34161e+04 5.57602e+04 7.65365e+02 -1.97155e+02 8.52248e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.06644e+05 8.46716e+04 -5.77343e+03 -1.11612e+06 -2.67240e+05 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -1.26284e+06 6.13687e+05 -6.49154e+05 8.17667e+02 -1.08370e+02 Pressure (bar) Constr. rmsd -8.62031e+04 5.99322e-04 Would you please give me any suggestions? Does my system need more equilibration yet? longer equilibration time? Whats the problem? My settings as sent you earlier seem fine, so whats the solution? Thanks for your suggestions. They would be appreciated. The temperature is 817 K, indicating something is moving with a ridiculously high velocity that has been imparted by strong forces. You have atoms overlapping somewhere. Try more thorough energy minimization. -Justin Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 7, 2013 4:46 PM Subject: Re: [gmx-users] unstable system On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Hi all, I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually. I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group . I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I don't get many pdb files to see. As what I see in Diagnosing unstable system web page, 1. it would be beneficial if one see what part of the system is unstable in first steps. As I saw, the unstable POPC hydrogen atoms are not fine. 2. The single molecules are supposed to examine in water or vacuum too. I have passed this step successfully. 3. I have not ignored any warning during the last steps. 4. And my mdp files to run md is as follow: integrator = md dt = 0.002 nsteps = 500 ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw
Re: [gmx-users] unstable system
Lets check the minim.mdp settings: ( ff applied is charmm36) define = -DPOSRES integrator = steep emtol = 100.0 emstep = 0.01 nsteps = 5 nstlist = 1 ns_type = grid rlist = 1.2 rlistlong = 1.4 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 vdwtype = switch rvdw_switch = 1.0 pbc = xyz I would be grateful for your suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 8:42 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:55 AM, Shima Arasteh wrote: All right. And if minimization doesnt fix such a problem, what would be the solution? However I have not tried it on my own system yet. It's a waste of time to delve into hypotheticals. Please try the advice you've been given and report back if needed. Crashes like you are seeing are almost invariably due to poor starting configuration. Thorough EM solves that problem. If, for some reason, that doesn't work, we will continue to diagnose. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 8:22 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:43 AM, Shima Arasteh wrote: Thanks for your reply. I' d like to know if I need to remove all position restraints before MDRUN?means that the last step of npt should be done without position restraints? Whatever makes sense for your system. There is no universal answer to how equilibration should be done. If your simulation is crashing at step zero, I doubt that removing restraints will help in any way. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 7:58 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:26 AM, Shima Arasteh wrote: Hi, I tried to equilibrate my system by setting timestep=1 fts and decreasing the position restraints step by step. But when I go to MDRUN step, it doesnt work and some pdb files are printed. what is printed in my log file is as follow: Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 8.34161e+04 5.57602e+04 7.65365e+02 -1.97155e+02 8.52248e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.06644e+05 8.46716e+04 -5.77343e+03 -1.11612e+06 -2.67240e+05 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -1.26284e+06 6.13687e+05 -6.49154e+05 8.17667e+02 -1.08370e+02 Pressure (bar) Constr. rmsd -8.62031e+04 5.99322e-04 Would you please give me any suggestions? Does my system need more equilibration yet? longer equilibration time? Whats the problem? My settings as sent you earlier seem fine, so whats the solution? Thanks for your suggestions. They would be appreciated. The temperature is 817 K, indicating something is moving with a ridiculously high velocity that has been imparted by strong forces. You have atoms overlapping somewhere. Try more thorough energy minimization. -Justin Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 7, 2013 4:46 PM Subject: Re: [gmx-users] unstable system On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Hi all, I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually. I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group . I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I don't get many pdb files to see. As what I see in Diagnosing unstable system web page, 1. it would be beneficial if one see what part of the system
Re: [gmx-users] unstable system
The energy minimization has been done and the result is as follow: Steepest Descents converged to Fmax 100 in 8971 steps Potential Energy = -1.5253394e+06 Maximum force = 9.2729095e+01 on atom 4719 Norm of force = 3.5977371e+00 But by running mdrun, I get this fatal error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. So needs more npt? Thanks for your suggestions in advance. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 10:02 PM Subject: Re: [gmx-users] unstable system On 4/19/13 1:18 PM, Shima Arasteh wrote: Lets check the minim.mdp settings: ( ff applied is charmm36) define = -DPOSRES integrator = steep emtol = 100.0 emstep = 0.01 nsteps = 5 nstlist = 1 ns_type = grid rlist = 1.2 rlistlong = 1.4 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 vdwtype = switch rvdw_switch = 1.0 pbc = xyz I would be grateful for your suggestions. I see no reason to use restraints (doing so defeats the purpose of EM), but otherwise the settings are fine. -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
Re: [gmx-users] unstable system
Thanks so much for your replies. I appreciate you. Do you think that more NPT equilibration might solve the problem? or wont work? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 11:23 PM Subject: Re: [gmx-users] unstable system On 4/19/13 2:49 PM, Shima Arasteh wrote: The energy minimization has been done and the result is as follow: Steepest Descents converged to Fmax 100 in 8971 steps Potential Energy = -1.5253394e+06 Maximum force = 9.2729095e+01 on atom 4719 Norm of force = 3.5977371e+00 But by running mdrun, I get this fatal error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. So needs more npt? I have no idea what this means. The minimization looks perfect. Continue with whatever equilibration scheme you think is appropriate. -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 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 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] unstable system
Yes, some letters were transferred by mistakes to email. Yes, I am using charmm36. Also the rvdw_switch was correct the same as you wrote 1.0 in last email. Now, I am wondering what the solution is in such cases of facing such an error? Would you please let me know your suggestions? Many thanks for your replies. Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, April 7, 2013 4:46 PM Subject: Re: [gmx-users] unstable system On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Hi all, I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually. I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group . I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I don't get many pdb files to see. As what I see in Diagnosing unstable system web page, 1. it would be beneficial if one see what part of the system is unstable in first steps. As I saw, the unstable POPC hydrogen atoms are not fine. 2. The single molecules are supposed to examine in water or vacuum too. I have passed this step successfully. 3. I have not ignored any warning during the last steps. 4. And my mdp files to run md is as follow: integrator = md dt = 0.002 nsteps = 500 ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 0.1 What force field are you using? CHARMM? In any case, the value of rvdw_switch does not make any sense. If you're using CHARMM, it should be 1.0. ; Parameters for treating bonded interactions continuation = yes constraint_algorithm = LINCS NCS / SHAKE) constraints = all-bonds ) lincs_iter = 1 lincs_order = 4 ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = Nose-Hoover tc-grps = Protein_POPC Water_and_ions ; Define groups to be coupled separately to temperature bath tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps) ref_t = 310 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Initial Velocity Generation gen_vel = no ; Centre of mass (COM) motion removal relative to the specified groups nstcomm = 1 y (steps) comm_mode = Linear comm_grps =Protein_POPC Water_and_ions ; COM removal relative to the specified groups Would you please let me know if these happen due to an improper equilibration? Do I need to extend the NPT step? Would that fix it? Aside from the above comment, there is nothing particularly wrong about the .mdp file aside from some odd characters here and there, which I will assume are nothing more than quirks of transferring to an email, as they otherwise would have triggered fatal errors in grompp. -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] unstable system
Hi all, I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually. I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group . I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I don't get many pdb files to see. As what I see in Diagnosing unstable system web page, 1. it would be beneficial if one see what part of the system is unstable in first steps. As I saw, the unstable POPC hydrogen atoms are not fine. 2. The single molecules are supposed to examine in water or vacuum too. I have passed this step successfully. 3. I have not ignored any warning during the last steps. 4. And my mdp files to run md is as follow: integrator = md dt = 0.002 nsteps = 500 ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 0.1 ; Parameters for treating bonded interactions continuation = yes constraint_algorithm = LINCS NCS / SHAKE) constraints = all-bonds ) lincs_iter = 1 lincs_order = 4 ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = Nose-Hoover tc-grps = Protein_POPC Water_and_ions ; Define groups to be coupled separately to temperature bath tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps) ref_t = 310 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Initial Velocity Generation gen_vel = no ; Centre of mass (COM) motion removal relative to the specified groups nstcomm = 1 y (steps) comm_mode = Linear comm_grps =Protein_POPC Water_and_ions ; COM removal relative to the specified groups Would you please let me know if these happen due to an improper equilibration? Do I need to extend the NPT step? Would that fix it? Thanks in advance. I appreciate your suggestions. Sincerely, Shima -- 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] water molecule can not be settled
Hi all, I am trying to simulate a system of protein and lipid bilayer ( in this case POPC). The ff I am using is CHARMM36 and I used related settings from literature. I used InflateGRO to pack the lipids around my protein. Then put a position restraint on my protein and P atoms of POPC. With these position restraints I ran NVT for 1ns and NPT for around10 ns. ( I need to say that NPT has been done in three steps: 1.First 5ns with position restraint on whole protein and P atoms 2. Then 3 ns with position restraint on just protein atoms 3. And finally 1 ns with position restraint on protein without H atoms. ) In fact, I tried to prevent any crash by sudden changes. Next, I tried to run MDRUN, but I get the error of some water molecules can not be settled. This means that my system has not been equiliberated sufficiently. OK, what should I do? How can I solve it? Water molecules can not be deleted in this step because I will get another fatal error as a result. My system seems fine. The pressure and energy plots don't show anything unusual. But I dont know how can I solve the problem. Would you please give me any suggestions? Reducing the timestep and also changing the thermostat could not help my system to overcome this problem. What would be the best solution? Sincerely, Shima -- 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
Fw: [gmx-users] water molecule can not be settled
I' d like to know if it is acceptable to change the molecule coordinates to solve this problem? Some time back, I deleted such a molecule and then I got a fatal error containing that the trj file and other inputs are not inconsistent. Would you please give me suggestions? I need them urgently. I really appreciate your help. Sincerely, Shima - Forwarded Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, April 5, 2013 6:25 PM Subject: [gmx-users] water molecule can not be settled Hi all, I am trying to simulate a system of protein and lipid bilayer ( in this case POPC). The ff I am using is CHARMM36 and I used related settings from literature. I used InflateGRO to pack the lipids around my protein. Then put a position restraint on my protein and P atoms of POPC. With these position restraints I ran NVT for 1ns and NPT for around10 ns. ( I need to say that NPT has been done in three steps: 1.First 5ns with position restraint on whole protein and P atoms 2. Then 3 ns with position restraint on just protein atoms 3. And finally 1 ns with position restraint on protein without H atoms. ) In fact, I tried to prevent any crash by sudden changes. Next, I tried to run MDRUN, but I get the error of some water molecules can not be settled. This means that my system has not been equiliberated sufficiently. OK, what should I do? How can I solve it? Water molecules can not be deleted in this step because I will get another fatal error as a result. My system seems fine. The pressure and energy plots don't show anything unusual. But I dont know how can I solve the problem. Would you please give me any suggestions? Reducing the timestep and also changing the thermostat could not help my system to overcome this problem. What would be the best solution? Sincerely, Shima -- 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 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
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? Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, April 5, 2013 7:42 PM Subject: Re: Fw: [gmx-users] water molecule can not be settled On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: I' d like to know if it is acceptable to change the molecule coordinates to solve this problem? It's unlikely that some ad hoc change will magically fix a problem. Energy minimization should take care of clashes. Some time back, I deleted such a molecule and then I got a fatal error containing that the trj file and other inputs are not inconsistent. Right, because you've now changed the contents of the system. It no longer matches the topology and the trajectory would then be discontinuous. -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
Re: Fw: [gmx-users] water molecule can not be settled
You mean start over the NPT step? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org 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 shima_arasteh2...@yahoo.comwrote: 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 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 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] Inactivate position restraint
Hi, To inactivate a position restraint, is it enough to make the define command in mdp file to a comment? ;define= DPOSRES Sincerely, Shima -- 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] position restraints
Hi Dear Justin First of all, I request you that not to shout at me! I am so sorry to ask you questions about position restraints again! I know I have sent you such emails before, and you suggested me to read include file mechanism in web site. I did this and also read some emails in forum. But I think I have problems with include mechanism. Again I got into the trouble about position restraining: As you told me -DPOSRES will not trigger #ifdef POSRE or #ifdef DPOSRES. I have a system of POPC/ions/waters and a double chain protein inserted in POPC bilayer. I put restraints on P headgroups and protein. I added the define line to the mdp file as follow: define = -DPOSRES_LIPID -DPOSRES Then added the itp files to my top as follow: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif But when I run the grompp with -pp flag, I see that restraints on chain_B are not included! Then I changed the numbering in protein_chain_B_posre.itp to what they are in their original itp file, generated earlier by pdb2gmx. Do you agree that it is the problem which I encountered with? Now when I run grompp I see the restraints after each chains with the same numbering. Sincerely, Shima Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 12:02 AM Subject: Re: [gmx-users] position restraints On 3/25/13 3:25 PM, Shima Arasteh wrote: Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly. Say I have a system of arbitrary molecules that have 4 atoms each. Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule. Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive. Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error. What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified. So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file. If, for instance, P is atom number 8: [ position_restraints ] 8 1 0 0 1000 That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only. Hopefully that all makes sense and this experience has been educational as far as how these things work. -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 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 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] position restraints
No, You have not shouted at me, never! But sometimes I think that I deserve to be shouted !! I deeply appreciate your patience and attention. Thanks for your time and your replies. In my protein, chains A and B are identical. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 4:16 PM Subject: Re: [gmx-users] position restraints On 3/26/13 7:01 AM, Shima Arasteh wrote: Hi Dear Justin First of all, I request you that not to shout at me! I am so sorry to ask you questions about position restraints again! I haven't done any shouting, but statements like this seem to imply that I have. The point of this forum is post your questions, so if things still aren't clear, then you're welcome to post them. Hopefully I have never given anyone the impression of anger or castigation in my answers. Sometimes I am terse, but that's because I'm busy with my own work, and a short answer is preferable to a long one. I know I have sent you such emails before, and you suggested me to read include file mechanism in web site. I did this and also read some emails in forum. But I think I have problems with include mechanism. Again I got into the trouble about position restraining: As you told me -DPOSRES will not trigger #ifdef POSRE or #ifdef DPOSRES. I have a system of POPC/ions/waters and a double chain protein inserted in POPC bilayer. I put restraints on P headgroups and protein. I added the define line to the mdp file as follow: define = -DPOSRES_LIPID -DPOSRES Then added the itp files to my top as follow: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif #ifdef POSRE requires -DPOSRE, not -DPOSRES as you have above. I've now said that three times (and you said it above!), so please be mindful of the advice you've been given and take care in what you're doing. ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif But when I run the grompp with -pp flag, I see that restraints on chain_B are not included! I don't see how that's possible. Position restraints for both chains are under the control of the same #ifdef condition, as shown above. One cannot be restrained without the other. Then I changed the numbering in protein_chain_B_posre.itp to what they are in their original itp file, generated earlier by pdb2gmx. Do you agree that it is the problem which I encountered with? pdb2gmx should have provided you with suitable restraint .itp files when you produced the original topology, and will have written suitable #ifdef blocks to properly use them. Have you manipulated these files in some way? If you have, start over. Use the files that pdb2gmx gave you until you can convince yourself that you know how to use them correctly, then apply whatever custom restraints you feel are necessary. Learn to walk before you run. Now when I run grompp I see the restraints after each chains with the same numbering. I don't exactly know what this means. Are chains A and B identical? If they are, then this makes sense. -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
Re: Fw: [gmx-users] position restraints
1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 MG 1 MG MG 1 2 [ moleculetype ] ; molname nrexcl K 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 POT 1 K K 1 1 [ moleculetype ] ; molname nrexcl Ces 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CES 1 Ces Ces 1 1 [ moleculetype ] ; molname nrexcl Cal 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CAL 1 Cal Cal 1 2 [ moleculetype ] ; molname nrexcl CL 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CLA 1 CL CL 1 -1 [ moleculetype ] ; molname nrexcl ZN 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 ZN 1 ZN ZN 1 -2 [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 18706 NA 615 CL 617 Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 9:55 PM Subject: Re: Fw: [gmx-users] position restraints On Tue, Mar 26, 2013 at 1:01 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Have a look at processed topology file here please; I see that position restraints are brought after chain_A but not brought after chain_B. With these settings: ; Include chain topologies #ifdef POSRES #include topol_Protein_chain_A.itp #include protein_chain_A_posre.itp #endif #ifdef POSRES #include topol_Protein_chain_B.itp #include protein_chain_B_posre.itp #endif The above approach is incorrect. The inclusion of protein topologies is dependent upon using position restraints? That's certainly not right, especially if you ever want to run a simulation without restraints. The following is the correct approach: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif Also adding define = -DPOSRES_LIPID -DPOSRES , I get this processed.top: #grompp -f nvt.mdp -c minim.gro -p topol.top -n index.ndx -o nvt.tpr -pp THIS IS THE PROCESSED TOPOLOGY: ; File 'topol.top' was generated ; By user: shima (1000) ; On host: linux-cbyo.site ; At date: Wed Dec 12 12:17:51 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p ; ; Force field was read from current directory or a relative path - path added. ; ; Include forcefield parameters ; Conversion of CHARMM36 parameters to GROMACS format by Thomas Piggot, July 2010. ; Also added some parameters from later CHARMM27 versions, such as those for the PS headgroup. ; ; If you use these parameters please check out the forcefield.doc for papers to cite [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 ; ; Added new and changed old atomtypes and pairtypes (OSL, OSLP, HBL and CCL) - Thomas Pigot July 2010 ; [ atomtypes ] ;name at.num mass charge ptype sigma epsilon C 6 12.01100 0.51 A 0.356359487256 0.46024 CA 6 12.01100 -0.115 A 0.355005321205 0.29288 CC 6 12.01100 0.62 A 0.356359487256 0.29288 CD 6 12.01100 0.000 A 0.356359487256 0.29288 ; partial charge def not found CE1 6 12.01100 0.000 A 0.372395664183 0.284512 ; partial charge def not found . . . . X NN1 CN1A X 9 180.0 10.46 2 X NN2 CN3B X 9 180.0 4.184 2 X CN3 CN3C X 9 180.0 0.4184 2 X NN2 CN3C X 9 180.0 0.4184 2 X ON4 P3 X 9 0.0 1.2552 3 [ dihedraltypes ] ; i j k l func q0 cq NN2B CN4 CN5 HN2 2 0.0 58.576 NN2G CN4 CN1 HN2 2 0.0 6.6944 NN1 CN2 HN1 HN1 2 0.0 50.208 CN1 NN2G CN5G ON1 2 0.0 753.12 CN1T NN2B NN2U ON1 2 0.0 920.48 CN1 NN2U CN3T ON1 2 0.0 753.12 CN2 NN3G NN2G NN1 2 0.0 334.72 CN2 NN3A CN5 NN1 2 0.0 334.72 CN2 NN3 CN3 NN1 2 0.0 502.08 CN4 NN2G NN3I HN3 2 0.0 326.352 CN3 CN3C CN8 HN6 2 0.0 125.52 HN2 CN3 CN3B NN2 2 0.0 418.4 HN1 HN1 CN1A
Re: Fw: [gmx-users] position restraints
Thanks for all your explanations. What I get as a conclusion is this: itp files are dependent to the numbering of aoms in molecule type directive and not any other things! Each posre.itp file created by genrestr should be in consistent with the molculetype numbering! Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, March 26, 2013 10:54 PM Subject: Re: Fw: [gmx-users] position restraints On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: The inclusion part was edited again in original top file. I dont know why I had written that! Sorry. But about last itp files, which you mentioned that they are created incorrectly, 1) I 'd like to know what itp file should be created? In my own, I just included the chain_B.itp file with the same numbering as the chain_A.itp file. I don't really know what that means. You should be using the files pdb2gmx gave you, at least until you understand how all of this works. You should not have to deal with anything related to restraining the protein. Hence why I've suggested that you start over. 2) One more thing, restraints for both chains are brought just one time in the processed.top file? I thought after each chain, the restraints which are included should be brought and written in processed.top file!!! They should. But what you showed makes no sense. Restraints can't correspond to atoms that don't exist and there should only ever be on [ position_restraints ] directive per [ moleculetype ]. -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 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 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] position restraints
Hi, I want to use position restraints on P atom types of POPC, and on my protein inserted in POPC. The inserted protein has 2 chains. 1. I made index files for each chain and then restrained them by these commands: #make_ndx -f minim.gro -o protein_chain_A.ndx #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 -n protein_chain_A.ndx #make_ndx -f minim.gro -o protein_chain_B.ndx #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 -n protein_chain_B.ndx #make_ndx -f minim.gro -o lipid_posre.ndx #genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n lipid_posre.ndx 2. Then these lines added to top of the itp files: #ifdef POSRE #endif 3. Then restrained them as follow in top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRE_LIPID #include lipid_posre.itp #endif 4. Also added the define statement to mdp file : define = -DPOSRES_LIPID -DPOSRES But when I run the grompp and get the per-processed top, only the chain_A is included in position restraint! Would you please give me suggestions? They would be appreciated. Thanks in advance. Sincerely, Shima -- 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] position restraints
Believe me I add this line to mdp file as you wrote in KALP-15-DPPC. define = -DPOSRES_LIPID Also added these to top file. #ifdef POSRES_LIPID #include lipid_posre.itp #endif But I get again this error that the This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :(( Would you please help me? Thanks for help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 8:52 PM Subject: Re: [gmx-users] position restraints On 3/25/13 12:06 PM, Shima Arasteh wrote: Hi, I want to use position restraints on P atom types of POPC, and on my protein inserted in POPC. The inserted protein has 2 chains. 1. I made index files for each chain and then restrained them by these commands: #make_ndx -f minim.gro -o protein_chain_A.ndx #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 10 10 10 -n protein_chain_A.ndx #make_ndx -f minim.gro -o protein_chain_B.ndx #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 10 10 10 -n protein_chain_B.ndx #make_ndx -f minim.gro -o lipid_posre.ndx #genrestr -f minim.gro -o lipid_posre.itp -fc 10 10 10 -n lipid_posre.ndx 2. Then these lines added to top of the itp files: #ifdef POSRE #endif 3. Then restrained them as follow in top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRE #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRE #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRE_LIPID #include lipid_posre.itp #endif 4. Also added the define statement to mdp file : define = -DPOSRES_LIPID -DPOSRES But when I run the grompp and get the per-processed top, only the chain_A is included in position restraint! Would you please give me suggestions? They would be appreciated. Again, POSRE and POSRES are different. -DPOSRES will not trigger the #ifdef POSRE block. -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
Re: [gmx-users] position restraints
Yes sir! What I have in my top file is : ; Include forcefield parameters #include ./charmm36-modified.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 18706 NA 615 CL 617 I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 10:13 PM Subject: Re: [gmx-users] position restraints On 3/25/13 1:40 PM, Shima Arasteh wrote: Believe me I add this line to mdp file as you wrote in KALP-15-DPPC. I believe what I see. If you're trying to re-type from memory what's in your topology and/or .mdp file, that's not productive. Please copy and paste to make efficient use of everyone's time. define = -DPOSRES_LIPID Also added these to top file. #ifdef POSRES_LIPID #include lipid_posre.itp #endif But I get again this error that the This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :(( Would you please help me? I've been trying, and it appears you're either giving inconsistent or incorrect information. Copy and paste directly from your .top file whatever sections are relevant. You also haven't said what is in lipid_posre.itp, which can be another source of problems. You just said you've created it with genrestr, but you didn't say what group you included. The numbering in the position restraint file is per [moleculetype], not the global atom numbering in the coordinate file. -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 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 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] position restraints
Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms? Thanks for your suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 10:22 PM Subject: Re: [gmx-users] position restraints On 3/25/13 1:50 PM, Shima Arasteh wrote: Yes sir! What I have in my top file is : ; Include forcefield parameters #include ./charmm36-modified.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif ; Include POPC chain topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include ./charmm36-modified.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include ./charmm36-modified.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 18706 NA 615 CL 617 I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know. In that case, lipid_posre.itp should have only one line. If you've made an index group of multiple P atoms across multiple molecules, that is the incorrect approach. Consult the manual, website, and numerous threads in the archive. -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
Re: [gmx-users] position restraints
Yes, you are right. Because I have read the include mechanism in website many times, but I dont undrestand it in deep! :-( I may need to study more. Thanks Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 11:20 PM Subject: Re: [gmx-users] position restraints On 3/25/13 2:47 PM, Shima Arasteh wrote: Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms? What you need to understand is how the position restraint mechanism works. If you know that, you can make .itp files by hand using a text editor if you like (which is actually what I do in the case of one-liners like lipid_posre.itp for what you're doing). -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 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 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] position restraints
Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, March 25, 2013 11:34 PM Subject: Re: [gmx-users] position restraints On 3/25/13 3:00 PM, Shima Arasteh wrote: Yes, you are right. Because I have read the include mechanism in website many times, but I dont undrestand it in deep! :-( I may need to study more. I would again suggest focusing more on the position restraints contents themselves. Your formulation for #including them is correct. The contents of lipid_posre.itp are not. There is substantial discussion on the topic of position restraints in the manual, as well as the help description of genrestr (especially the part that starts with WARNING), which I am willing to bet will solve your issues if you read it carefully. -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
Re: [gmx-users] position restraints
Ohhh...! :-) I could not get it on my own independently! Thanks for all your explanation! Many many thanks. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 12:02 AM Subject: Re: [gmx-users] position restraints On 3/25/13 3:25 PM, Shima Arasteh wrote: Dear Justin, As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file. Am I right? More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly. Say I have a system of arbitrary molecules that have 4 atoms each. Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule. Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive. Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error. What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified. So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file. If, for instance, P is atom number 8: [ position_restraints ] 8 1 0 0 1000 That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only. Hopefully that all makes sense and this experience has been educational as far as how these things work. -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 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 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] gro does not match top
Hi, I am solving a protein in water. This protein has a charge of +3. After solvation there is 3272 water molecules. Next, I use genion command to add NACL 1M and 3 extra CL ions to neutralize the system. #genion -s ions.tpr -o cyclic_solv_ions.gro -p topol.top -nname CL -nn 3 -conc 1 After this, the top file shows: Protein_chain_A 1 SOL 3147 NA 61 CL 61 CL 3 But when I check the cyclic_solv_ions.gro file, there are 60 NA and 60 CL ions! Therefore the top doesnt match with gro file and I get the fatal error. What' s your suggestions? How does it come? Thanks in advance. Sincerely, Shima -- 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] Re: gro does not match top
In fact the genion does not add the neutralizing CL ions to gro file! Why? How can I solve this problem? Would you please help me? Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, March 24, 2013 5:16 PM Subject: gro does not match top Hi, I am solving a protein in water. This protein has a charge of +3. After solvation there is 3272 water molecules. Next, I use genion command to add NACL 1M and 3 extra CL ions to neutralize the system. #genion -s ions.tpr -o cyclic_solv_ions.gro -p topol.top -nname CL -nn 3 -conc 1 After this, the top file shows: Protein_chain_A 1 SOL 3147 NA 61 CL 61 CL 3 But when I check the cyclic_solv_ions.gro file, there are 60 NA and 60 CL ions! Therefore the top doesnt match with gro file and I get the fatal error. What' s your suggestions? How does it come? Thanks in advance. Sincerely, Shima -- 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] Re: gro does not match top
Thanks! I did! :-) Sincerely, Shima From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Sunday, March 24, 2013 9:50 PM Subject: Re: [gmx-users] Re: gro does not match top On Sun, Mar 24, 2013 at 2:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/24/13 9:02 AM, Shima Arasteh wrote: In fact the genion does not add the neutralizing CL ions to gro file! Why? How can I solve this problem? Using -nn and -conc is probably incompatible, because -conc will add some number of ions, which may not play nicely with the fact that you are then manually saying add only 3 negative ions with -nn 3. The correct formation of the command is to use genion -conc 1 -neutral. If Shima had read genion -h, there is a description of -conc that announces that it overrides -nn and -np. Mark -- 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] define statement in mdp file
Hi, I need to set position restraints on phosphorus head groups of lipids in addition of protein. In mdp file I added two lines: define = -DPOSRES define= -DPOSRES_LIPID But I get the error that multiple define assignments are not allowed. Is the define= -DPOSRES_LIPID is enough for both protein and headgroups? Thanks in advance. Sincerely, Shima -- 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] define statement in mdp file
That's right. But I' d like to be sure about this fact that both restraints are applied. I see just 1 position restraints energy term in log file. Is just visualizing the trr file the only way of becoming sure that the headgroups and protein are restrained? And one more question is that, to eliminating the position restraints in MDRUN, is it supposed to reduce the force on atoms before mdrun gradually? Or it is ok to reduce it in MD step? Thanks for your suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Saturday, March 23, 2013 10:37 PM Subject: Re: [gmx-users] define statement in mdp file On 3/23/13 8:59 AM, Shima Arasteh wrote: Hi, I need to set position restraints on phosphorus head groups of lipids in addition of protein. In mdp file I added two lines: define = -DPOSRES define= -DPOSRES_LIPID But I get the error that multiple define assignments are not allowed. Is the define= -DPOSRES_LIPID is enough for both protein and headgroups? Not likely, but that depends on the construction of your .top. I will assume that each #define statement controls a separate topology, which is a good idea. The correct approach is to specify as many define statements as you like on one line (this is really just stolen from cpp): define = -DPOSRES -DPOSRES_LIPID -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
Re: [gmx-users] Top file modification
Dears, As I read in some other messages in mailing list, it is supposed to modify bonds, angles and dihedrals in top file to define a peptide bond for the last and first residues as well as other peptide bonds. I am wondering if it is necessary to define pairs too? Thanks in advance. Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, March 19, 2013 9:11 PM Subject: Re: [gmx-users] Top file modification On Tue, Mar 19, 2013 at 1:36 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Would you please let me know if it is acceptable to add dihedrals and angles and bonds? and not to add any pairs to the top? just deleting the pairs which are added by pdb2gmx incorrectly to the terminus? And I don't know that if I don't add all bonds or dihedrals what would happen? How would I be sure that I have added all modifications completely? All you're doing is creating a peptide bond like any other. Its description should be identical to any other peptide bond in the protein. An incorrect or incomplete description of the newly created peptide bond would mean an unreliable physical model that would either crash or produce spurious results. -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] T-Coupling groups in NVT
Hi, I am simulating a system of POPC/Water/Ions/protein. Ions are 1 M NaCL and 3 CL atoms to neutralize the system. In NVT step, I have coupling groups as : tc-grps = Protein POPC SOL_CL comm_grps = Protein_POPC SOL_CL when I run the grompp for NVT, I get the error that the 615 Na atoms are not part of any of the T-Coupling groups. Now, I 'd like to know if I need to couple Na with SOL_CL such as SOL_CL-Na ? Or I need to create a seperate group for Na? Would you please give me suggestions? Thanks in advance. Sincerely, Shima -- 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] T-Coupling groups in NVT
So accordance with Justin's and your statement, SOL_CL_NA coupling would be a proper option. right? Thanks for your suggestions Sincerely, Shima From: Gunther Lukat g.lu...@gmx.net To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, March 21, 2013 4:31 PM Subject: Re: [gmx-users] T-Coupling groups in NVT I general, I have good results with coupling Ions together with the water. Dipl.-Inf. Gunther Lukat g.lu...@gmx.net www.aplvoro.org Am 21.03.2013 um 13:56 schrieb Shima Arasteh shima_arasteh2...@yahoo.com: Hi, I am simulating a system of POPC/Water/Ions/protein. Ions are 1 M NaCL and 3 CL atoms to neutralize the system. In NVT step, I have coupling groups as : tc-grps = Protein POPC SOL_CL comm_grps = Protein_POPC SOL_CL when I run the grompp for NVT, I get the error that the 615 Na atoms are not part of any of the T-Coupling groups. Now, I 'd like to know if I need to couple Na with SOL_CL such as SOL_CL-Na ? Or I need to create a seperate group for Na? Would you please give me suggestions? Thanks in advance. Sincerely, Shima -- 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 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] atom numbers in top file
Dear gmx users, I have modified the top file of my input.pdb. In this modification I have deleted 2 atoms, bonds, and diedrals which these deldeted atoms are involved. The atom numbers of deleted atoms are 2 and 3. IN grompp I get a fatal error that the top file has not a consecutive numbers and doesn't start from 1. Would it be possible to solve this problem? Am I supposed to renumber the atoms and other things manually? Is there any command to renumber the top file? Or is there any other solutions? your suggestions would be appreciated. Sincerely, Shima -- 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] Top file modification
Dear users, I modified my top file, because I didn't want some bonds. So I deleted them and changed charges on some atoms. I want to go on with such a top file, however I am not sure that these changes are implemented properly or not. Would you please let me know if what I did is right or not? And how would I be sure about the proper modifications? Thanks in advance for all your beneficial suggestions. Sincerely, Shima -- 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] Top file modification
:) In fact, I have a NMR pdb file of a cyclic peptide. To get a proper gro and topology files, I ran pdb2gmx without -ter flag. Then tried to modify the top file. Is there any better ideas? Thanks for your reply. Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, March 19, 2013 8:51 PM Subject: Re: [gmx-users] Top file modification On Tue, Mar 19, 2013 at 1:07 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear users, I modified my top file, because I didn't want some bonds. So I deleted them and changed charges on some atoms. I want to go on with such a top file, however I am not sure that these changes are implemented properly or not. Would you please let me know if what I did is right or not? And how would I be sure about the proper modifications? Making ad hoc changes to topologies or force fields is generally a bad idea unless you have thoroughly validated what you are doing with a correct parameterization procedure. What you've described above (especially given the lack of specificity) sounds very dangerous. If you want advice, be specific as to exactly what you are doing. It is your job to convince a skeptical audience (e.g., reviewers) that what you're doing makes sense and thus you must have strong justification for it. Somebody on the Internet told me it was OK is generally not an acceptable defense ;) -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
Re: [gmx-users] Top file modification
Would you please let me know if it is acceptable to add dihedrals and angles and bonds? and not to add any pairs to the top? just deleting the pairs which are added by pdb2gmx incorrectly to the terminus? And I don't know that if I don't add all bonds or dihedrals what would happen? How would I be sure that I have added all modifications completely? Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Tuesday, March 19, 2013 9:00 PM Subject: Re: [gmx-users] Top file modification On Tue, Mar 19, 2013 at 1:28 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: :) In fact, I have a NMR pdb file of a cyclic peptide. To get a proper gro and topology files, I ran pdb2gmx without -ter flag. Then tried to modify the top file. Is there any better ideas? Manual modification in that case is probably reasonably safe, as long as you are careful to use parameters that are appropriate for all bonded and nonbonded interactions that change as a result of the modification. -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] Function of dihedrals in top file
Dears, There is term of function for each 4 atoms in dihedral section in top file. How this function is defined? To add extra dihedrals manually, I need to add function too. Thanks. Sincerely, Shima -- 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] Function of dihedrals in top file
As I found up to now, func 2 is related to improper dihedrals. How can I find improper dihedrals? Can I not add them? Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 19, 2013 9:46 PM Subject: [gmx-users] Function of dihedrals in top file Dears, There is term of function for each 4 atoms in dihedral section in top file. How this function is defined? To add extra dihedrals manually, I need to add function too. Thanks. Sincerely, Shima -- 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 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: Fwd: Fw: Fwd: [gmx-users] position restraints
To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the fatal error. This error states that I have inserted topology section position_restraints in a wrong place. I checked again the itp files included in my top file. They are matched correctly! Did I modified the settings incorrectly? What would be other potent problems? Please help me. Thanks for your help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, March 17, 2013 5:19 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/17/13 6:50 AM, Shima Arasteh wrote: Thanks for your replies. As you suggested, I did as follows: 1. made index groups of two chains of my protein 2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -n index-chain.ndx 3.Next, I included the itp files as follow in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef DPOSRE #include chainA_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef DPOSRE #include chainB_posre.itp #endif 4. I also added this line to my mdp file: define = -DPOSRE 5. In addition I added these at the top of itp files for bothe restrained chains: #ifdef DPOSRE #endif Now when I run the command : grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr I don't get any errors. But when I run the mdrun I don't see any position restraint terms in my log file. Would you please let me know your suggestions in this about? Did I do any steps by mistake? Yes, again there is a problem with the #ifdef statements. If you use: #ifdef DPOSRE ... #endif the corresponding define statement is -DDPOSRE. Think of the first D in the define statement as I am defining the following string to be true. Your .mdp file corresponds to the use of: #ifdef POSRE ... #endif -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
Re: Fwd: Fw: Fwd: [gmx-users] position restraints
Thanks for all your replies. But I' d like to know what the meanings of S and D are? Why sometimes we should write DPOSRE, sometimes POSRE, and sometimes DPOSRES? Sincerely, Shima From: Shima Arasteh shima_arasteh2...@yahoo.com To: Justin Lemkul jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, March 18, 2013 10:35 AM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the fatal error. This error states that I have inserted topology section position_restraints in a wrong place. I checked again the itp files included in my top file. They are matched correctly! Did I modified the settings incorrectly? What would be other potent problems? Please help me. Thanks for your help. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, March 17, 2013 5:19 PM Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints On 3/17/13 6:50 AM, Shima Arasteh wrote: Thanks for your replies. As you suggested, I did as follows: 1. made index groups of two chains of my protein 2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp #genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 10 10 10 -n index-chain.ndx #genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 10 10 10 -n index-chain.ndx 3.Next, I included the itp files as follow in my top file: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef DPOSRE #include chainA_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef DPOSRE #include chainB_posre.itp #endif 4. I also added this line to my mdp file: define = -DPOSRE 5. In addition I added these at the top of itp files for bothe restrained chains: #ifdef DPOSRE #endif Now when I run the command : grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr I don't get any errors. But when I run the mdrun I don't see any position restraint terms in my log file. Would you please let me know your suggestions in this about? Did I do any steps by mistake? Yes, again there is a problem with the #ifdef statements. If you use: #ifdef DPOSRE ... #endif the corresponding define statement is -DDPOSRE. Think of the first D in the define statement as I am defining the following string to be true. Your .mdp file corresponds to the use of: #ifdef POSRE ... #endif -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 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 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
