Re: [gmx-users] Freeze group atoms changing position
Just as an update, I ran the simulation using position restraints with force constants set to 1 for each atom in the restrained waters, and none jumped out of the nanotube. Thanks for the help! On Thu, Nov 1, 2012 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/1/12 4:56 PM, Alex Marshall wrote: I've created a position restraint file for the specific waters that I need to immobilize, but I'm having a hard time getting grompp to apply it successfully. No matter where I put #include posre.itp in my topology file grompp returns fatal errors about the atomic indices being out of bounds. Is it actually possible to only apply position restraints to some molecules within a species and leave the rest alone? Yes, but you can't simply #include spc.itp and then call the position restraint file, for example. You need a [moleculetype] for the entire block of water, since position restraints can only be applied per [moleculetype]. -Justin On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/12 3:55 PM, Alex Marshall wrote: Chris, is that for freeze groups or position restraints? I will assume Chris was referring to the restraint method - you need an index file for creating the position restraint .itp file using genrestr. It will save you a ton of time over doing it manually. -Justin On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: No need to rename... just make an .ndx group. -- original message -- As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall amarsh59 at uwo.ca wrote: Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu bcostescu at gmail.comwrote: On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amarsh59 at uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Are you using some kind of constraints ? Are you using energy group exclusions to avoid interactions between frozen atoms ? If you search the manual for frozen you'll find some warnings and recommendations. Cheers, Bogdan -- gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searchhttp://www.gromacs.org/**Support/Mailing_Lists/Search
Re: [gmx-users] Freeze group atoms changing position
I've created a position restraint file for the specific waters that I need to immobilize, but I'm having a hard time getting grompp to apply it successfully. No matter where I put #include posre.itp in my topology file grompp returns fatal errors about the atomic indices being out of bounds. Is it actually possible to only apply position restraints to some molecules within a species and leave the rest alone? On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/12 3:55 PM, Alex Marshall wrote: Chris, is that for freeze groups or position restraints? I will assume Chris was referring to the restraint method - you need an index file for creating the position restraint .itp file using genrestr. It will save you a ton of time over doing it manually. -Justin On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: No need to rename... just make an .ndx group. -- original message -- As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall amarsh59 at uwo.ca wrote: Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu bcostescu at gmail.comwrote: On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amarsh59 at uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Are you using some kind of constraints ? Are you using energy group exclusions to avoid interactions between frozen atoms ? If you search the manual for frozen you'll find some warnings and recommendations. Cheers, Bogdan -- gmx-users mailing listgmx-users at gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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
Re: [gmx-users] Freeze group atoms changing position
As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall amars...@uwo.ca wrote: Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu bcoste...@gmail.comwrote: On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amars...@uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Are you using some kind of constraints ? Are you using energy group exclusions to avoid interactions between frozen atoms ? If you search the manual for frozen you'll find some warnings and recommendations. Cheers, Bogdan -- 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 -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- 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] Freeze group atoms changing position
No need to rename... just make an .ndx group. -- original message -- As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall amarsh59 at uwo.ca wrote: Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu bcostescu at gmail.comwrote: On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amarsh59 at uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Are you using some kind of constraints ? Are you using energy group exclusions to avoid interactions between frozen atoms ? If you search the manual for frozen you'll find some warnings and recommendations. Cheers, Bogdan -- gmx-users mailing listgmx-users at 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-request at gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- 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] Freeze group atoms changing position
Chris, is that for freeze groups or position restraints? On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: No need to rename... just make an .ndx group. -- original message -- As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall amarsh59 at uwo.ca wrote: Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu bcostescu at gmail.comwrote: On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amarsh59 at uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Are you using some kind of constraints ? Are you using energy group exclusions to avoid interactions between frozen atoms ? If you search the manual for frozen you'll find some warnings and recommendations. Cheers, Bogdan -- gmx-users mailing listgmx-users at 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-request at gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- 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 -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- 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] Freeze group atoms changing position
On 10/31/12 3:55 PM, Alex Marshall wrote: Chris, is that for freeze groups or position restraints? I will assume Chris was referring to the restraint method - you need an index file for creating the position restraint .itp file using genrestr. It will save you a ton of time over doing it manually. -Justin On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: No need to rename... just make an .ndx group. -- original message -- As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall amarsh59 at uwo.ca wrote: Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu bcostescu at gmail.comwrote: On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amarsh59 at uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Are you using some kind of constraints ? Are you using energy group exclusions to avoid interactions between frozen atoms ? If you search the manual for frozen you'll find some warnings and recommendations. Cheers, Bogdan -- gmx-users mailing listgmx-users at 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-request at gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- 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 -- 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] Freeze group atoms changing position
Well, I thought that it would work for for freeze groups, and that is what I intended to say. I've used freeze groups before, but don't have tonnes of experience with them. The gromacs mdp options page reads as if it should work ( http://manual.gromacs.org/online/mdp_opt.html#neq ), but if Justin says that you can not use an index group for freeze groups (only position restraints) then I suggest that you take his word for it. He answers a lot more posts and is probably more familiar with the ins and outs of gromacs. Chris,. -- original message -- Alex Marshall amarsh59 at uwo.ca Wed Oct 31 20:55:08 CET 2012 Previous message: [gmx-users] Freeze group atoms changing position Next message: [gmx-users] Freeze group atoms changing position Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Chris, is that for freeze groups or position restraints? On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale chris.neale at mail.utoronto.ca wrote: No need to rename... just make an .ndx group. -- original message -- As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks -- 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] Freeze group atoms changing position
On 10/31/12 4:21 PM, Christopher Neale wrote: Well, I thought that it would work for for freeze groups, and that is what I intended to say. I've used freeze groups before, but don't have tonnes of experience with them. The gromacs mdp options page reads as if it should work ( http://manual.gromacs.org/online/mdp_opt.html#neq ), but if Justin says that you can not use an index group for freeze groups (only position restraints) then I suggest that you take his word for it. He answers a lot more posts and is probably more familiar with the ins and outs of gromacs. That's not what I meant at all. One can use an index group for freeze groups, as well. The original problem was that apparently the frozen group was not working entirely, so I suggested (as a troubleshooting measure) that the OP use restraints instead to see if the outcome was different. The bizarre behavior before (two molecules moving, but the remainder staying frozen) suggested to me that perhaps there was something going wrong with the initial configuration and I was hoping that, at the very least, using restraints would determine if the configuration was messed up or not amenable to freezing. -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] Freeze group atoms changing position
makes sense. -- original message -- On 10/31/12 4:21 PM, Christopher Neale wrote: Well, I thought that it would work for for freeze groups, and that is what I intended to say. I've used freeze groups before, but don't have tonnes of experience with them. The gromacs mdp options page reads as if it should work ( http://manual.gromacs.org/online/mdp_opt.html#neq ), but if Justin says that you can not use an index group for freeze groups (only position restraints) then I suggest that you take his word for it. He answers a lot more posts and is probably more familiar with the ins and outs of gromacs. That's not what I meant at all. One can use an index group for freeze groups, as well. The original problem was that apparently the frozen group was not working entirely, so I suggested (as a troubleshooting measure) that the OP use restraints instead to see if the outcome was different. The bizarre behavior before (two molecules moving, but the remainder staying frozen) suggested to me that perhaps there was something going wrong with the initial configuration and I was hoping that, at the very least, using restraints would determine if the configuration was messed up or not amenable to freezing. -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] Freeze group atoms changing position
Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu bcoste...@gmail.comwrote: On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amars...@uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Are you using some kind of constraints ? Are you using energy group exclusions to avoid interactions between frozen atoms ? If you search the manual for frozen you'll find some warnings and recommendations. Cheers, Bogdan -- 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 -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- 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] Freeze group atoms changing position
Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. On Wed, Oct 24, 2012 at 9:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/12 3:17 PM, Alex Marshall wrote: Hi all, I'm simulating a system of two reservoirs connected by a carbon nanotube. The reservoir wall atoms and carbon nanotube atoms are held in place using freeze groups at all times. I'm currently equilibrating the reservoirs separately by also freezing the water inside the nanotube, but after 20 ns two of the frozen water molecules have jumped outside of the nanotube into a supposedly inaccessible region. What could cause this? Should I be worried? I would be. Frozen groups aren't supposed to move at all. Verify that the problematic water molecules are indeed contained within whatever frozen group(s) you have assigned in the .mdp file. Otherwise, there's no immediate explanation, especially since other frozen atoms are staying frozen. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- 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] Freeze group atoms changing position
On 10/25/12 9:59 AM, Alex Marshall wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Then I'm stumped. Freezing shouldn't partially work - either it does or doesn't, and I've never seen anything like this. As a test, do simple position restraints fare better? -Justin On Wed, Oct 24, 2012 at 9:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/12 3:17 PM, Alex Marshall wrote: Hi all, I'm simulating a system of two reservoirs connected by a carbon nanotube. The reservoir wall atoms and carbon nanotube atoms are held in place using freeze groups at all times. I'm currently equilibrating the reservoirs separately by also freezing the water inside the nanotube, but after 20 ns two of the frozen water molecules have jumped outside of the nanotube into a supposedly inaccessible region. What could cause this? Should I be worried? I would be. Frozen groups aren't supposed to move at all. Verify that the problematic water molecules are indeed contained within whatever frozen group(s) you have assigned in the .mdp file. Otherwise, there's no immediate explanation, especially since other frozen atoms are staying frozen. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Freeze group atoms changing position
On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amars...@uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. Are you using some kind of constraints ? Are you using energy group exclusions to avoid interactions between frozen atoms ? If you search the manual for frozen you'll find some warnings and recommendations. Cheers, Bogdan -- 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] Freeze group atoms changing position
Hi all, I'm simulating a system of two reservoirs connected by a carbon nanotube. The reservoir wall atoms and carbon nanotube atoms are held in place using freeze groups at all times. I'm currently equilibrating the reservoirs separately by also freezing the water inside the nanotube, but after 20 ns two of the frozen water molecules have jumped outside of the nanotube into a supposedly inaccessible region. What could cause this? Should I be worried? -- Thanks, Alex Marshall M.Sc -- 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] Freeze group atoms changing position
On 10/24/12 3:17 PM, Alex Marshall wrote: Hi all, I'm simulating a system of two reservoirs connected by a carbon nanotube. The reservoir wall atoms and carbon nanotube atoms are held in place using freeze groups at all times. I'm currently equilibrating the reservoirs separately by also freezing the water inside the nanotube, but after 20 ns two of the frozen water molecules have jumped outside of the nanotube into a supposedly inaccessible region. What could cause this? Should I be worried? I would be. Frozen groups aren't supposed to move at all. Verify that the problematic water molecules are indeed contained within whatever frozen group(s) you have assigned in the .mdp file. Otherwise, there's no immediate explanation, especially since other frozen atoms are staying frozen. -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] freeze group
I running the simulation of a protein with Fe4s4 cluster. The parameters for the cluster were obtained from a previously published paper. I have been able to carry out energy minimization with the following keywords- ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no -- The output showsSteepest Descents converged to Fmax 2000 in 203 steps Potential Energy = -5.8639745e+06 Maximum force = 1.7305787e+03 on atom 777 Norm of force = 4.4084099e+01 But when I am trying the position retraining step, with following keywords in pr.mdp file- title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20.0 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.4 ; Berendsen temperature coupling is on Tcoupl = v-rescale tc-grps = Protein SOL SF4 tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein SOL SF4 ; Pressure coupling is on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 an error is generated with LINCS warningStep 155, time 0.31 (ps) LINCS WARNING relative constraint deviation after LINCS: rms inf, max 14002532367890120704.00 (between atoms 5093 and 5096) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1193 1195 40.1 0.1330 0.1913 0.1330 1193 1194 38.7 0.1230 0.1757 0.1230 1191 1192 77.7 0.1530 210.9258 0.1530 1189 1193 63.7 0.1530 193.1889 0.1530 1189 1190 75.9 0.1530 193.1568 0.1530 1188 1192 65.6 0.1470 893.4214 0.1470 1188 1189 67.7 0.1470 909.7200 0.1470 1186 1188 72.8 0.1330 3701.8413 0.1330 1186 1187 78.6 0.1230 3824.8157 0.1230 1184 1185 79.5 0.1780 57.6559 0.1780 1183 1184 79.3 0.1829 539.6799 0.1830 1182 1183 85.5 0.1530 3695.6021 0.1530 1181 1186 84.6 0.1530 14910.0859 0.1530 1181 1182 86.6 0.1530 15403.3672 0.1530 1179 1181 87.4 0.1470 35502.0234 0.1470 1179 1180 89.9 0.1000 1119163.2500 0.1000 1177 1179 86.7 0.1330 37732.0156 0.1330 1177 1178 85.9 0.1230 17608.4004 0.1230 1175 1177 99.6 0.1530 50041.0938 0.1530 1175 1176 102.3 0.1530 37907.5586 0.1530 1173 1175 117.7 0.1470 698413.0625 0.1470 1173 1174 120.6 0.1000 677364.4375 0.1000 1171 1173 107.2 0.1330 4168765.5000 0.1330 1171 1172 108.5 0.1230 4103918.2500 0.1230 1169 1170 112.9 0.1090 9872814. 0.1090 1167 1169 92.1 0.1390 68041384. 0.1390t = 0.310 ps: Water molecule starting at atom 196197 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates - These atoms 5093 and 5096 are the Iron atoms of the cluster. Now My question is- a) Can I freeze the movement of the Fe4S4 cluster during simulation by incorporating the cluster in freeze group? b) If yes, then how do I incorporate the freeze group in Pr.mdp file during position restraining step? c) Is there any other alternative to correct the linc warning error? The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] freeze group
subarna thakur wrote: I running the simulation of a protein with Fe4s4 cluster. The parameters for the cluster were obtained from a previously published paper. I have been able to carry out energy minimization with the following keywords- snip *a) Can I freeze the movement of the Fe4S4 cluster during simulation by incorporating the cluster in freeze group?* Can I? and should I? are separate concepts. Of course you can, but would that be useful? See below. *b) If yes, then how do I incorporate the freeze group in Pr.mdp file during position restraining step?* Please read the manual. *c) Is there any other alternative to correct the linc warning error?* I would suggest several things before trying to freeze the cluster artificially. First, choose a more stringent energy minimization criterion. Fmax 2000 is typically insufficient for almost any system. Also, having the cluster as its own separate temperature coupling group is inappropriate. See here, specifically the second point under What Not To Do: http://www.gromacs.org/Documentation/Terminology/Thermostats -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] freeze group gives Segmentation fault
I just tried Gromacs 4.0.2. It still gives a Segmentation fault: Reading file topol.tpr, VERSION 4.0.2 (single precision) Loaded with Money Segmentation fault I did a test, putting the whole system into one freezegroup. Then the simulation starts running. But some of the atoms belonging to the freeze-group still move: The RMSD keeps growing and the Potential Energy = -132 kJ/mol. Reading in the trajectory with vmd shows the molecules moving. There is no pattern in the motion though. I checked the index.ndx twice - there is no mistake in there. Ilona There was a bug in the freeze group code that got fixed today. I don't know anything else about it. Please update your source code and try again. Mark [EMAIL PROTECTED] wrote: Using freezegroups I get a Segmentation fault. The simulation does not start, so the output is empty. Reading file topol.tpr, VERSION 4.0_rc4 (single precision) Segmentation fault ; ; File 'mdout.mdp' was generated ; By user: bq_ibaldus (2417) ; On host: cln-fg06 ; At date: Fri Nov 7 15:53:11 2008 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= none ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 0.01 emstep = 0.01 ; Max number of iterations in relax_shells niter= 100 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 1 nstfout = 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = crystal ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.5 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off rcoulomb_switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii =
RE: [gmx-users] freeze group gives Segmentation fault
Hi, I don't understand your mail. Do you really get a segmentation fault, but also frames in your trajectory file? I think I fixed the freezing of the whole system bug. I tested it for a water system and it runs fine. Maybe you have constraints in your system. Asking your system to be completely frozen and to obey the constraints is usually contradictory. Therefore you system might still move slightly to try to obey the constraints. Anyhow it seems pretty useless to me to simulate a completely frozen system. Berk From: [EMAIL PROTECTED] Date: Mon, 10 Nov 2008 15:13:06 +0100 To: gmx-users@gromacs.org Subject: Re: [gmx-users] freeze group gives Segmentation fault I just tried Gromacs 4.0.2. It still gives a Segmentation fault: Reading file topol.tpr, VERSION 4.0.2 (single precision) Loaded with Money Segmentation fault I did a test, putting the whole system into one freezegroup. Then the simulation starts running. But some of the atoms belonging to the freeze-group still move: The RMSD keeps growing and the Potential Energy = -132 kJ/mol. Reading in the trajectory with vmd shows the molecules moving. There is no pattern in the motion though. I checked the index.ndx twice - there is no mistake in there. Ilona There was a bug in the freeze group code that got fixed today. I don't know anything else about it. Please update your source code and try again. Mark [EMAIL PROTECTED] wrote: Using freezegroups I get a Segmentation fault. The simulation does not start, so the output is empty. Reading file topol.tpr, VERSION 4.0_rc4 (single precision) Segmentation fault _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] freeze group gives Segmentation fault
Hi! I am trying to use freezegroups on an ice-crystal. grompp gives no warning. Trying the same simulation but removing the freezegroup works. Please note my mdp-file's attached Ilona ; ; File 'mdout.mdp' was generated ; By user: bq_ibaldus (2417) ; On host: cln-fg06 ; At date: Fri Nov 7 15:53:11 2008 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= none ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 0.01 emstep = 0.01 ; Max number of iterations in relax_shells niter= 100 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 1 nstfout = 1 ; Output frequency for energies to log file and energy file nstlog = 1 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = crystal ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.5 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off rcoulomb_switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = Berendsen ; Groups to couple separately tc_grps = crystal ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t
Re: [gmx-users] freeze group gives Segmentation fault
[EMAIL PROTECTED] wrote: Hi! I am trying to use freezegroups on an ice-crystal. grompp gives no warning. Trying the same simulation but removing the freezegroup works. We're not mind-readers :-) Why do you think it's not working? What do you see on stdout? In the various output files? Please note my mdp-file's attached That's a start. It's a bit like taking one's car to the mechanic. The fact that you brought it in means you think something's probably wrong, but it'll cost you a lot more or take lots more time if you don't tell them things you've found out. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] freeze group
Hello wisdoms! We are performing the simulation of a protein of which the ion is surrounded by three aminoacids with in nearly 3A distance. Is it right to set my ion in the freeze group since it moves out of box during EM steps Else is there any strategy to fix the bug so that the coordinate bond cant be affected during the simulation. Thany You, Kindly Regards, E.Elavazhagan. -- Bio [EMAIL PROTECTED] -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] freeze group
Hello wisdoms! We are performing the simulation of a protein of which the ion is surrounded by three aminoacids with in nearly 3A distance. Is it right to set my ion in the freeze group since it moves out of box during EM steps Else is there any strategy to fix the bug so that the coordinate bond cant be affected during the simulation. If I understand you correctly, you want the ion to stay within the coordination sphere of the three amino acids. If so then you want to be using distance restraints of some kind... probably a harmonic bond. See table 5.4 and then look around chapters 4 and 5. You can even use LINCS to constrain them to a specific length, once a bond exists. By the way, speaking strictly you don't have a bug, which would be a problem with the structure of the gromacs code. You are having a problem telling the simulation to do what you want it to do. Hard-working developers can get annoyed when you use the word bug, which ascribes to them a fault that is almost assuredly your own :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
