Re: Re: [gmx-users] steered pulling code on ligand-receptor complex
Thank you so much! > -原始邮件- > 发件人: "Jianguo Li" > 发送时间: 2012年10月31日 星期三 > 收件人: "Discussion list for GROMACS users" > 抄送: > 主题: Re: [gmx-users] steered pulling code on ligand-receptor complex > > If you position restraint the receptor or only use several residues at the > binding site, in both cases you limit your sampling to a small part of the > phase space and the PMF may not be accurate, since the receptor may undergo > conformational change upon ligand binding. > Cheers > --Jianguo > > > > - Original Message - > From: 范聪 > To: gmx-users@gromacs.org > Cc: > Sent: Tuesday, 30 October 2012, 20:04 > Subject: [gmx-users] steered pulling code on ligand-receptor complex > > > Hello, everyone! > I'm a new user in gromacs, and now I have to perform a steered pulling > code on a ligand-receptor complex. The ligand is to be pulled away from the > binding site of the receptor, and umbrella sampling will be used to gain the > PMF (potential mean force) curve. Then binding energy of the ligand-receptor > complex would be estimated. The receptor contains 303 residues. While the > ligand is pulling away, the whole receptor is restrained by posres, 1000 in > x, y and z axis. > Since the receptor is so large and umbrella sampling needs so much > calculations, a very long time will be taken to complete the work. > Now I have my question, is there anyway to reduce the taken time? Such as > keeping only residues near the binding site to respect the whole receptor? > Thank you all in advance! > > -- > 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 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] Gmx Hessian
hi Gmxers, is the Hessian matrix unit in gmx is ps^(-2), or J *mol^(-1) nm^(-2)? thanks, Yao -- 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_rdf
Dear Ali: I don't think that you are re-posting the same question often enough. Perhaps you should repost more often? 4 identical posts in 5 hours might not be enough to get a reply Seriously though, we all saw your message. Chris. -- original message(s) -- I have a system that contains water , methane and propane in 240 k and 300 bar, My simulation box is rectangular . Water film is in middle of my box. Methane and propane is around it. My simulation box is symmetric, 1- I used g_rdf program for . My result is exotic. My g(r) in profile do not reach to 1 . Why ? 2- I test my number density profiles(from g_density) but they do not correct result because when i calculate number of my molecules by multiplying volume to average number density, i can not take the same number of my particle, Where do i mistake? -- Sincerely Ali Alizadeh -- Sincerely Ali Alizadeh -- 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_rdf
On 10/31/12 4:56 PM, Ali Alizadeh wrote: Dear All users I have a system that contains water , methane and propane in 240 k and 300 bar, My simulation box is rectangular . Water film is in middle of my box. Methane and propane is around it. My simulation box is symmetric, 1- I used g_rdf program for . My result is exotic. My g(r) in profile do not reach to 1 . Why ? "Exotic" is not a useful description. Are there systematic trends? Bumps in the plot? What's going on? What groups are you choosing for the analysis? It seems to me the asymmetry in the system will cause some odd behavior in an RDF, but without seeing an actual plot (i.e. a picture) then it's hard to comment. 2- I test my number density profiles(from g_density) but they do not correct result because when i calculate number of my molecules by multiplying volume to average number density, i can not take the same number of my particle, From the extensive posts on this topic in recent days, you should know that there are issues with g_density. -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
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
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 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 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 gmail.com>wrote: On Thu, Oct 25, 2012 at 3:59 PM, 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. 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
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 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 gmail.com>wrote: > > > >> On Thu, Oct 25, 2012 at 3:59 PM, 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. > >> > >> 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
[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 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 gmail.com>wrote: > >> On Thu, Oct 25, 2012 at 3:59 PM, 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. >> >> 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
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 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 wrote: > >> On Thu, Oct 25, 2012 at 3:59 PM, 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. >> >> 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] What exactly is the artifact caused by setting refcoord_scaling=no with position restraint
I've asked the same question myself and would also like to know. That said, there seems to be no issue if you set refcoord_scaling=com. According to the manual, this does not give artefacts (whatever they are) and also does not change your restraint positions (as refcoord_scaling=all does). Sorry that I can't give a complete answer, but, to my understanding, refcoord_scaling=no is probably just there for backward compatibility and you should use refcoord_scaling=com. Hopefully somebody who knows the full answer can comment. Chris. -- original message -- After reading the manual and some earlier threads, I understand that this would cause incorrect pressure and some "artifact". I found gromacs4.5.4 does not give warning while gromacs4.5.5 does? But I wonder how large would the average pressure deviate when setting refcoord_scaling=no compared when setting refcoord_scaling=com/ all, with absolute position restraints? Does the pressure reported in .log file still correct when setting refcoord_scaling=no? Thanks, Yun -- 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: Error in npt run - box size/ triclinic skew factor
On 10/31/12 12:38 PM, mtso wrote: Just make sure whatever changes you are making are correct for the chosen force field and algorithms. If you're having problems with NPT, you can always switch to the Berendsen algorithm for pressure coupling before returning to Parrinello-Rahman for data collection. -Justin Thanks for the quick response, I've changed to the Berendsen algorithm, and still get the same error message. When looking at the files we've used in the past for similar simulations, the file we use for annealing has pressure coupling off. Would it even be necessary to do NPT before annealing then? You didn't mention annealing before, that would have been helpful to know. So the .mdp file you posted before is not one that is causing a problem? I'm just lost as to what you're doing now. Doing annealing using NPT may become unstable, depending upon how happy the system is to start and how drastic the temperature changes are. NVT is probably more stable for annealing. -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] Re: Error in npt run - box size/ triclinic skew factor
>Just make sure whatever changes you are making are correct for the chosen force >field and algorithms. If you're having problems with NPT, you can always switch >to the Berendsen algorithm for pressure coupling before returning to >Parrinello-Rahman for data collection. -Justin Thanks for the quick response, I've changed to the Berendsen algorithm, and still get the same error message. When looking at the files we've used in the past for similar simulations, the file we use for annealing has pressure coupling off. Would it even be necessary to do NPT before annealing then? -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-npt-run-box-size-triclinic-skew-factor-tp5002482p5002507.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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/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] testing Gromacs 4.6 (git version) on GPUs
Thank you! Yes, I am able to run the 'dhfr-solv-PME.bench' benchmark with mdrun -s topol.tpr -testverlet and it seems to be using the GPUs as well: --- 2 GPUs detected: #0: NVIDIA Tesla M2050, compute cap.: 2.0, ECC: yes, stat: compatible #1: NVIDIA Tesla M2050, compute cap.: 2.0, ECC: yes, stat: compatible 2 GPUs auto-selected to be used for this run: #0, #1 --- Best, Susan. On Oct 31, 2012, at 12:15 PM, Roland Schulz wrote: > Hi, > > you can use the tpr files from the tgz if you use the non-implicit "solv" > (preferable PME) test. > > Roland > > On Wed, Oct 31, 2012 at 10:37 AM, Susan Chacko wrote: > >> >> Hi all, >> >> I wanted to test the built-in support in Gromacs 4.6 (non-OpenMM) for GPUs. >> I downloaded the latest git version and it built successfully, appears >> to link the right CUDA libraries etc. >> >> I tried testing it with the Gromacs GPU benchmark suite >> (http://www.gromacs.org/@api/deki/files/128/=gromacs-gpubench-dhfr.tar.gz) >> >> The output md.log file reports: >> >> […] >> NOTE: GPU(s) found, but the current simulation can not use GPUs >> To use a GPU, set the mdp option: cutoff-scheme = Verlet >> (for quick performance testing you can use the -testverlet option) >> >> >> So I tried 'mdrun -s topol.tpr -testverlet' and got: >> --- >> Program mdrun, VERSION 4.6-dev >> Source code file: /usr/local/src/gromacs/gromacs/src/kernel/runner.c, >> line: 700 >> >> Fatal error: >> Can only convert old tpr files to the Verlet cut-off scheme with 3D pbc >> For more information and tips for troubleshooting, please check the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> --- >> >> Does anyone have a test set that I can use to check the performance of >> Gromacs 4.6 on GPUs? I'm more of a sysadmin than a computational chemist, >> so I'm sort of reliant on the provided benchmark suites. >> >> Any suggestions welcomed and appreciated, >> Susan. >> >> >> -- >> 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 >> >> >> >> >> > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > -- > 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 Susan Chacko Helix/Biowulf Staff -- 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] testing Gromacs 4.6 (git version) on GPUs
Hi, you can use the tpr files from the tgz if you use the non-implicit "solv" (preferable PME) test. Roland On Wed, Oct 31, 2012 at 10:37 AM, Susan Chacko wrote: > > Hi all, > > I wanted to test the built-in support in Gromacs 4.6 (non-OpenMM) for GPUs. > I downloaded the latest git version and it built successfully, appears > to link the right CUDA libraries etc. > > I tried testing it with the Gromacs GPU benchmark suite > (http://www.gromacs.org/@api/deki/files/128/=gromacs-gpubench-dhfr.tar.gz) > > The output md.log file reports: > > […] > NOTE: GPU(s) found, but the current simulation can not use GPUs > To use a GPU, set the mdp option: cutoff-scheme = Verlet > (for quick performance testing you can use the -testverlet option) > > > So I tried 'mdrun -s topol.tpr -testverlet' and got: > --- > Program mdrun, VERSION 4.6-dev > Source code file: /usr/local/src/gromacs/gromacs/src/kernel/runner.c, > line: 700 > > Fatal error: > Can only convert old tpr files to the Verlet cut-off scheme with 3D pbc > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > Does anyone have a test set that I can use to check the performance of > Gromacs 4.6 on GPUs? I'm more of a sysadmin than a computational chemist, > so I'm sort of reliant on the provided benchmark suites. > > Any suggestions welcomed and appreciated, > Susan. > > > -- > 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 > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] About Doubt in Lipid protein Solvation
On 10/31/12 11:45 AM, vidhya sankar wrote: Dear Justin Thank you For your Previous Kind Reply I am following your Lipid-protein Tutorial for My system I Gave The Following Commands As Quoted in your Tutorial Also I Have Suitably Edited The Topology As in the Tutorial Now the Problem in My solvation . I Gave The Following Commands As Quoted in your Tutorial ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c ./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3 -box 6 6 6 ./grompp_d -f emdppc.mdp -c dppc128n.gro -p topol_dppc.top -o emdppc.tpr -maxwarn 1 ./trjconv_d -s emdppc.tpr -f dppc128n.gro -o dppc128_whole.gro -pbc mol -ur compact ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c cat 2KDQ_newbox.gro dppc128_whole.gro > system.gro ./genrestr_d -f 2KDQ_newbox.gro -o strong_posre.itp -fc 10 10 10 perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top -o 2KDQDPPCem.tpr ./mdrun_d -v -deffnm 2KDQDPPCem perl inflategro.pl 2KDQDPPCem.gro 0.95 DPPC 0 system_inflated1.gro 5 area1.dat I Repeated the inflate and EM Until I have Attained APL 66 (Experimental value 62) At the End of EMinimised .gro file The Box vectors Has been Increased form 6 6 6 6 to 20.57700 20.57700 6.0 What do you mean "at the end of EM?" Is this the first energy minimization of the inflated system, or the final minimization of the satisfactorily shrunken system? If the latter, something is clearly wrong as it is impossible to have such a large x-y area with the quoted APL. As result Box Size Also Increase When I solvate By mere Editing the Vanderwalls Radii to 0.470, then my system is is solvated By 64495 Water moleculesHow to Avoid this Problem ? This is too high Where I have Committed Mistakes I need your Valuable Ideas and Suggestions I have no idea. Your box size increases when you solvate? That makes no sense. Your description is not clear to me. -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] About Doubt in Lipid protein Solvation
Dear Justin Thank you For your Previous Kind Reply I am following your Lipid-protein Tutorial for My system I Gave The Following Commands As Quoted in your Tutorial Also I Have Suitably Edited The Topology As in the Tutorial Now the Problem in My solvation . I Gave The Following Commands As Quoted in your Tutorial ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c ./editconf_d -f dppc128.pdb -o dppc128n.gro -center 3 3 3 -box 6 6 6 ./grompp_d -f emdppc.mdp -c dppc128n.gro -p topol_dppc.top -o emdppc.tpr -maxwarn 1 ./trjconv_d -s emdppc.tpr -f dppc128n.gro -o dppc128_whole.gro -pbc mol -ur compact ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c cat 2KDQ_newbox.gro dppc128_whole.gro > system.gro ./genrestr_d -f 2KDQ_newbox.gro -o strong_posre.itp -fc 10 10 10 perl inflategro.pl system.gro 4 DPPC 18 system_inflated.gro 5 area.dat ./grompp_d -f emdppc.mdp -c system_inflated.gro -p 2KDQ.top -o 2KDQDPPCem.tpr ./mdrun_d -v -deffnm 2KDQDPPCem perl inflategro.pl 2KDQDPPCem.gro 0.95 DPPC 0 system_inflated1.gro 5 area1.dat I Repeated the inflate and EM Until I have Attained APL 66 (Experimental value 62) At the End of EMinimised .gro file The Box vectors Has been Increased form 6 6 6 6 to 20.57700 20.57700 6.0 As result Box Size Also Increase When I solvate By mere Editing the Vanderwalls Radii to 0.470, then my system is is solvated By 64495 Water molecules How to Avoid this Problem ? This is too high Where I have Committed Mistakes I need your Valuable Ideas and Suggestions Thanks In Advance . -- 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] time-block analysis
Leila, I provided 2 good references to answer your question earlier. If you can't be bothered to read about it, then the answer is yes, it is a good method. Looking at your other questions, I think that it is time for you to look at those references and learn more about block averaging and convergence in general. Chris. -- original message -- Thanks for your quick reply. You did not answer me (is block averaging good way for investigation of the simulation convergence?) Based on your example (histogram of the distribution of a dihedral angle), if I want to investigate convergence of RMSD, Figure 1 is RMSD vs time. But I dont know about Figure S1. what parameter vs what parameter (RMSD vs what)? Please describe more. If the value of [rms (quantity)/quantity] be less than 10 exp (-3), can I use that as convergence criterion? (for example, quantity= potential energy) Best regards -- 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, density
Dear Ali:
I am not sure what ecenter is, it looks like it might be the position to which
the user wants to set the center?
In any event, it doesn't mater for this modification.
I did not write the center_x() function, it is a standard part of gmx_trjconv.c
What I did was to copy center_x() to
center_x_com() and then modify center_x_com() such that it computes the center
of mass and not the position of
(max-min)/2.
I then modified the call to center_x() to actually be a call to center_x_com(),
where it requires the additional
argument of "atoms->atom" at the end of the list.
What I posted here:
http://lists.gromacs.org/pipermail/gmx-users/2011-June/062239.html is actually
the non-
modified function call from the original gmx_trjconv.c in gromacs 4.5.3 (posted
to show that there is a problem).
Here is a patch that you can apply to gromacs version 4.5.3 (but possibly not
to 4.5.4 or 4.5.5 because they made
slight other modifications to gmx_trjconv.c so I am not sure if this patch will
work). Still, it is just 2 blocks of changes
so once you understand them you can make the changes by hand.
--- ../../../../gromacs-4.5.3b/source/src/tools/gmx_trjconv.c 2010-09-29
07:35:06.0 -0400
+++ ./gmx_trjconv.c 2011-08-02 13:13:00.0 -0400
@@ -385,6 +385,33 @@
}
}
+static void center_x_com(int ecenter,rvec x[],matrix box,int n,int nc,atom_id
ci[],t_atom atom[])
+{
+int i,m,ai;
+rvec com,box_center,dx;
+real mtot;
+
+mtot=0.0;
+com[0]=com[1]=com[2]=0.0;
+if (nc > 0) {
+for(i=0; iatom);
+}
}
if (bPBCcomAtom) {
PATCH IS OVER
In case the patch is mangled by email formatting, you can try to just add the
lines yourself. Just add the
center_x_com() function and then use the call to center_x_com() and not
center_x() in the "if(bCenter)" sataement.
Note that there is the additional argument "atoms->atom" in the call to
center_x_com().
Chris.
-- original message --
I find out where you change the trjconv, I have a question
"ecenter" in this code, Where do you use it? and What is the ecenter?
static void center_x(int ecenter,rvec x[],matrix box,int n,int nc,atom_id
ci[])
{
int i,m,ai;
rvec cmin,cmax,box_center,dx;
if (nc > 0) {
copy_rvec(x[ci[0]],cmin);
copy_rvec(x[ci[0]],cmax);
for(i=0; i cmax[m])
cmax[m]=x[ai][m];
}
}
calc_box_center(ecenter,box,box_center);
for(m=0; mhttp://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] testing Gromacs 4.6 (git version) on GPUs
Hi all, I wanted to test the built-in support in Gromacs 4.6 (non-OpenMM) for GPUs. I downloaded the latest git version and it built successfully, appears to link the right CUDA libraries etc. I tried testing it with the Gromacs GPU benchmark suite (http://www.gromacs.org/@api/deki/files/128/=gromacs-gpubench-dhfr.tar.gz) The output md.log file reports: […] NOTE: GPU(s) found, but the current simulation can not use GPUs To use a GPU, set the mdp option: cutoff-scheme = Verlet (for quick performance testing you can use the -testverlet option) So I tried 'mdrun -s topol.tpr -testverlet' and got: --- Program mdrun, VERSION 4.6-dev Source code file: /usr/local/src/gromacs/gromacs/src/kernel/runner.c, line: 700 Fatal error: Can only convert old tpr files to the Verlet cut-off scheme with 3D pbc For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Does anyone have a test set that I can use to check the performance of Gromacs 4.6 on GPUs? I'm more of a sysadmin than a computational chemist, so I'm sort of reliant on the provided benchmark suites. Any suggestions welcomed and appreciated, Susan. -- 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: Error in npt run - box size/ triclinic skew factor
On 10/31/12 10:23 AM, mtso wrote: Thanks Justin, We're using the tutorial, and those .mdp files as a starting point but actually running the simulations on the protein PDB ID 2LFM, without adding a ligand for now, and modifying the .mdp files as necessary. Just make sure whatever changes you are making are correct for the chosen force field and algorithms. If you're having problems with NPT, you can always switch to the Berendsen algorithm for pressure coupling before returning to Parrinello-Rahman for data collection. -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] Re: Error in npt run - box size/ triclinic skew factor
Thanks Justin, We're using the tutorial, and those .mdp files as a starting point but actually running the simulations on the protein PDB ID 2LFM, without adding a ligand for now, and modifying the .mdp files as necessary. -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-npt-run-box-size-triclinic-skew-factor-tp5002482p5002494.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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/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] time-block analysis
Technically, in order to show that your simulation has reached complete convergence, you would need to show that every type of data has converged. Obviously nobody does this. You should start with looking at the convergence of any data type that you analyze in any other way. i.e. if you show a histogram of the distribution of a dihedral angle as Figure 1, then Figure S1 might be some analysis of the convergence of that histogram. Look at papers where people are doing similar things to what you are doing. Unfortunately, lots of otherwise good papers don't even consider convergence so you may need to do a little digging. PS: g_analyze sounds like a good idea. I've always scripted my own because it is more flexible, but if there is a gromacs tool to do this then use it. Chris. -- original message -- Very thanks for your reply. In addition of your suggested script, in the gromacs, -ee option of g_analyze produces error estimates using block averaging. A person suggest me to do time-block analysis to find that my simulation has converged or not. You mentioned to "2-column data file that has time in the first column and some other data in the second column". To investigate convergence of simulation, what should be as other data in mentioned file (2-column data file)? Any help will highly appreciated. -- 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] fraction of native contacts calculation
On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. -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] Why potential energy not in negative value?
On 10/31/12 4:10 AM, Nur Syafiqah Abdul Ghani wrote: Dear All, Currently I'm doing the minimization part for my solvent which is hexafluoroisopropanol with water. I'm packing them with packmol then use the forcefield gromos96. Now by using the command grompp -f em1.mdp -c minimize_301012.gro -p topol.top -o minimize_311012.tpr mdrun -deffnm minimize_311012 -v And its give the result as follow : writing lowest energy coordinates. Back Off! I just backed up minimize_311012.gro to ./#minimize_311012.gro.3# Steepest Descents converged to Fmax < 15 in 36 steps Potential Energy = 1.88042503678994e+05 Maximum force = 1.46843345643871e+01 on atom 30092 Norm of force = 1.94397813942079e+00 I already minimize it with the bigger step that use about 10ns. Next I increase the step which take about 15ns and the result show same as above.. Note that EM is not run in time, so your settings below are misleading. The only settings that matter are nsteps and emstep; dt is ignored completely when running EM. Note that your cutoff settings are incorrect for Gromos96, as you say you are using. How did you generate the HFIP topology? The positive potential indicates that your system has a net repulsive energy, so the configuration isn't very happy. The maximum force is very good, but there may be unsatisfied interactions that yield the positive energy. Perhaps a gentle equilibration will resolve the situation. -Justin My mdp file was like this : ; ; Preprocessing title= STEEP cpp = /usr/bin/cpp include = -I/usr/local/gromacs/share/gromacs/top define = -DFLEXIBLE ; ; Run Control ; integrator = steep nsteps = 7500 ; 7500 * 0.2 = 15000 ps = 15 ns dt = 0.0002 ; 0.2 fs ; ; Energy Minimization emstep = 0.0001 ; used with steep emtol= 15 nstcgsteep = 500 ; do a steep every 10 steps of cg energygrps = System ; ; Neighbor Searching nstcomm = 1 nstlist = 10 ns_type = grid pbc = xyz rlist= 1.2 ; ; Electrostatics coulombtype = pme rcoulomb = 1.2 rcoulomb-switch = 0 vdw-type = cut-off rvdw = 1.2 rvdw-switch = 0 fourierspacing = 0.2 ; ; Output Control nstenergy = 10 optimize_fft = yes ; ; OPTIONS FOR BONDS ; OPTIONS FOR BONDS constraints = none Is the potential energy need to be in negative value for my simulation? What happened if it not in negative value?Can I just proceed to the next step for equilibration? I already find and read the paper that relate to my simulation and they did not mention the energy that they got from their experiment. Thanks in advance u guys, -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. 013-7188131 alternative email : syafiqahabdulgh...@gmail.com -- 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] Error in npt run - box size/ triclinic skew factor
On 10/30/12 4:23 PM, mtso wrote: When trying to do an npt run, I get the fatal error: The X-size of the box (3.999511) times the triclinic skew factor (1.00) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.00). I should mention, I'm brand new to using gromacs so any assistance is greatly appreciated. My nvt run was fine. I used the following mdp file: The error means your system has become unstable and is about to blow up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up Are you running the tutorial? The .mdp file would indicate you are, but the system is very robust and I have not seen this happen. -Justin title = OPLS Lysozyme NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints = all-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 = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; 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 = V-rescale ; modified Berendsen thermostat tc-grps = Protein ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar refcoord_scaling= com ; scale center of mass of reference coordinates compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off Thanks in advance. -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-npt-run-box-size-triclinic-skew-factor-tp5002482.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] fraction of native contacts calculation
Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. *-- --- Thanks and Regards, Bipin Singh* -- 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] steered pulling code on ligand-receptor complex
If you position restraint the receptor or only use several residues at the binding site, in both cases you limit your sampling to a small part of the phase space and the PMF may not be accurate, since the receptor may undergo conformational change upon ligand binding. Cheers --Jianguo - Original Message - From: 范聪 To: gmx-users@gromacs.org Cc: Sent: Tuesday, 30 October 2012, 20:04 Subject: [gmx-users] steered pulling code on ligand-receptor complex Hello, everyone! I'm a new user in gromacs, and now I have to perform a steered pulling code on a ligand-receptor complex. The ligand is to be pulled away from the binding site of the receptor, and umbrella sampling will be used to gain the PMF (potential mean force) curve. Then binding energy of the ligand-receptor complex would be estimated. The receptor contains 303 residues. While the ligand is pulling away, the whole receptor is restrained by posres, 1000 in x, y and z axis. Since the receptor is so large and umbrella sampling needs so much calculations, a very long time will be taken to complete the work. Now I have my question, is there anyway to reduce the taken time? Such as keeping only residues near the binding site to respect the whole receptor? Thank you all in advance! -- 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
