Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass itamar.k...@monash.edu wrote: HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much. It is just the fact that I am trying to give as much info as I can and to go over any idea in the mailing list without actually delay my other stuff. So again, I wish thanks for anyone who is helps here. On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote: Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers or by ruling out possibilities. It is actually useful information to know that Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others ... but when it seems like you don't want to provide the requested information my first inclination is to give up on trying to help. At this point, there are a few unanswered old questions and I have some new questions. 1. Can you reproduce this with a water box? The error is reproducible in a box of protein and water only. 2. Can you reproduce this with your protein in vacuum? The error is reproduced in vacuum. 3. If neither 2 or 3, then can you step slowly from one of these systems toward your final system and identify the point at which the lincs warnings arise? 4. Do you get the warnings without Ca also, or just with Ca? I am not sure what this mean. I get this warning mainly for N-H, but also for Ca-C, pairs of atoms 5. Can you reproduce this with the SD integrator? If you are really against trying this, then at least can you reproduce this with a single Berendsen temperature coupling group? When I use SD integrator, the simulations run fine. 6. Can you reproduce this without using the reaction field? Either with PME or a simple cutoff? Using PME the system is running just fine. 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where you start to see this warning? I can't tell, 'cause I jump from 4.0.7 to 4.5.4. Thanks for the help, Itamar Chris. -- original message -- Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find. Itamar On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote: Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic may be different. It's important to rule out different variables to arrive at a solution, which I suspect is of interest to you. You also haven't addressed points #1 and #6 in Chris' message. -Justin Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000 LINCS, but this is usually a sign that something bad is going on in the system. OK. Chris suggested a number of other strategies that will help determine which aspect of 4.5.4 is behaving differently. How did those strategies work out? Mark Cheers, Itamar On 18/08/2011, at 12:03 PM, chris.neale at utoronto.ca wrote: OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just water or remove the ions, etc? 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 4.5.4. Do you get the
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass itamar.k...@monash.edu wrote: HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much. It is just the fact that I am trying to give as much info as I can and to go over any idea in the mailing list without actually delay my other stuff. So again, I wish thanks for anyone who is helps here. On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote: Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers or by ruling out possibilities. It is actually useful information to know that Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others ... but when it seems like you don't want to provide the requested information my first inclination is to give up on trying to help. At this point, there are a few unanswered old questions and I have some new questions. 1. Can you reproduce this with a water box? The error is reproducible in a box of protein and water only. 2. Can you reproduce this with your protein in vacuum? The error is reproduced in vacuum. 3. If neither 2 or 3, then can you step slowly from one of these systems toward your final system and identify the point at which the lincs warnings arise? 4. Do you get the warnings without Ca also, or just with Ca? I am not sure what this mean. I get this warning mainly for N-H, but also for Ca-C, pairs of atoms 5. Can you reproduce this with the SD integrator? If you are really against trying this, then at least can you reproduce this with a single Berendsen temperature coupling group? When I use SD integrator, the simulations run fine. 6. Can you reproduce this without using the reaction field? Either with PME or a simple cutoff? Using PME the system is running just fine. 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where you start to see this warning? I can't tell, 'cause I jump from 4.0.7 to 4.5.4. Thanks for the help, Itamar Chris. -- original message -- Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find. Itamar On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote: Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic may be different. It's important to rule out different variables to arrive at a solution, which I suspect is of interest to you. You also haven't addressed points #1 and #6 in Chris' message. -Justin Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
Hi Itamar, Yes, it appears that the 4.5.x series is more sensitive, due to the pressure coupling at intervals rather than at every step. Unfortunately the way it is now tied in with calculations of energies and neighbour searching indeed means that having nstpcouple set at 1 results in low simulation speeds. I find that the best approach is to equilibrate the system using a scheme as suggested to allow the system to get used to every perturbation (TC turned on, PC turned on, PC applied at intervals). Especially for the last step, the system has to 'get used' to having the pressure adjusted every nth step. The same holds for the transition from 4.0.7 to 4.5.x; it's in a sense a slight change of regime, to which the system has to get used. You can extend the simulation for a short period using nstpcouple=1, and then push it up higher again. Hope it helps, Tsjerk On Thu, Sep 1, 2011 at 10:32 AM, Itamar Kass itamar.k...@monash.edu wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass itamar.k...@monash.edu wrote: HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much. It is just the fact that I am trying to give as much info as I can and to go over any idea in the mailing list without actually delay my other stuff. So again, I wish thanks for anyone who is helps here. On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote: Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers or by ruling out possibilities. It is actually useful information to know that Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others ... but when it seems like you don't want to provide the requested information my first inclination is to give up on trying to help. At this point, there are a few unanswered old questions and I have some new questions. 1. Can you reproduce this with a water box? The error is reproducible in a box of protein and water only. 2. Can you reproduce this with your protein in vacuum? The error is reproduced in vacuum. 3. If neither 2 or 3, then can you step slowly from one of these systems toward your final system and identify the point at which the lincs warnings arise? 4. Do you get the warnings without Ca also, or just with Ca? I am not sure what this mean. I get this warning mainly for N-H, but also for Ca-C, pairs of atoms 5. Can you reproduce this with the SD integrator? If you are really against trying this, then at least can you reproduce this with a single Berendsen temperature coupling group? When I use SD integrator, the simulations run fine. 6. Can you reproduce this without using the reaction field? Either with PME or a simple cutoff? Using PME the system is running just fine. 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where you start to see this warning? I can't tell, 'cause I jump from 4.0.7 to 4.5.4. Thanks for the help, Itamar Chris. -- original message -- Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find. Itamar On
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk -- 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] GROMACS 4.5.4 keep crashing all the time
Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rendering such simulations less stable. As for SD, probably that causes sufficient damping of jitter introduced due to pressure coupling for it not to propagate and cause problems. But those are just my two cents (about 2.8 dollar cents with current rates :p). Cheers, Tsjerk On Thu, Sep 1, 2011 at 2:41 PM, chris.ne...@utoronto.ca wrote: I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not sure why PME would run fine and reaction field would give lincs warnings, but then again I have no experience with using a reaction field. Chris. On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] GROMACS 4.5.4 keep crashing all the time
On 2/09/2011 12:59 AM, chris.ne...@utoronto.ca wrote: That all makes sense Tsjerk. I wonder if mdrun terminations based on LINCS warnings should come with an additional message to explain that one may try running for a while with nstpcouple=1. That tip might be a good thing for the wiki page on that. Also, I'm still a little curious about a question that Itamar asked a few posts ago: If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? Mark provided a good explanation about how this could be possible, but I've never seen lincs warnings or systems blowing up after 5 ns of equilibration. I fully realize that it may take even us of simulation to properly equilibrate statistical properties, but in my experience it is far outside of ordinary to require 5 ns of equilibration to avoid systems blowing up. It's hard to say without more detail of how the extension occurred, and knowing how much ensemble data got lost. It's still conceivable some horrible mismatch occurred (e.g. virial over-written by some other data), but not really worth exploring properly. I'd just expect to have to re-equilibrate upon changing code version, and just not attempt such an extension. Mark Chris. -- original message -- Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rendering such simulations less stable. As for SD, probably that causes sufficient damping of jitter introduced due to pressure coupling for it not to propagate and cause problems. But those are just my two cents (about 2.8 dollar cents with current rates :p). Cheers, Tsjerk On Thu, Sep 1, 2011 at 2:41 PM, chris.neale at utoronto.ca wrote: I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not sure why PME would run fine and reaction field would give lincs warnings, but then again I have no experience with using a reaction field. Chris. On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT can be wise when the system starts far from equilibrium. Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data collected till now? If this is the case, why 5 ns simulations done with 4.0.7 crashed when extended it using 4.5.4? IIRC 4.0.x and 4.5.x have different mechanisms for deciding how often to do global communication for things like T and P coupling. Mostly you can get away with the same kind of approximation one uses with twin-range neighbour lists, periodic neighbour list updates, RESPA, etc. where slowly-varying quantities don't have to be recalculated every step. However during equilibration (and that includes the transition from 4.0.x to 4.5.x) those assumptions need not be valid. So tuning the update frequency to be high during transitions is a good idea. Then relax them and see how you go. Mark Also, is this mean I can do my productive run using 4.5.4 with the default value of nstpcouple, it seems that setting it to 1 greatly increases the computational time. To the best of my knowledge, in prior version nstpcouple was set to 1 by default. Cheers, Itamar On 01/09/2011, at 4:47 PM, Tsjerk Wassenaar wrote: Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may need to extend your equilibration a bit, first relaxing NVT, followed by NPT with nstpcouple=1, thereafter equilibrating using productions conditions. It it solves it, maybe the option should be renamed nstptrouble :p Hope it helps, Tsjerk -- 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 thewww interface or send it to gmx-users-request aGROMACS 4.5.4 keep crashing all the time Tsjerk Wassenaar tsjerkw at gmail.com Thu Sep 1 15:48:40 CEST 2011 * Previous message: [gmx-users] GROMACS 4.5.4 keep crashing all the time * Next message: [gmx-users] Non-zero total charge * Messages sorted by: [ date ] [ thread ] [
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000 LINCS, but this is usually a sign that something bad is going on in the system. Cheers, Itamar On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote: OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just water or remove the ions, etc? 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 4.5.4. Do you get the same lincs warnings? 6. Also, note that you are getting warnings and the run does not actually crash but just stops after too many warnings. So what are atoms 981 and 982? Does their motion look different in an important ways between the 4.0.7 and 4.5.4 trajectories? Chris. -- original message -- Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote: run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] GROMACS 4.5.4 keep crashing all the time
On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000 LINCS, but this is usually a sign that something bad is going on in the system. OK. Chris suggested a number of other strategies that will help determine which aspect of 4.5.4 is behaving differently. How did those strategies work out? Mark Cheers, Itamar On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote: OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just water or remove the ions, etc? 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 4.5.4. Do you get the same lincs warnings? 6. Also, note that you are getting warnings and the run does not actually crash but just stops after too many warnings. So what are atoms 981 and 982? Does their motion look different in an important ways between the 4.0.7 and 4.5.4 trajectories? Chris. -- original message -- Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote: run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] GROMACS 4.5.4 keep crashing all the time
Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000 LINCS, but this is usually a sign that something bad is going on in the system. OK. Chris suggested a number of other strategies that will help determine which aspect of 4.5.4 is behaving differently. How did those strategies work out? Mark Cheers, Itamar On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote: OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just water or remove the ions, etc? 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 4.5.4. Do you get the same lincs warnings? 6. Also, note that you are getting warnings and the run does not actually crash but just stops after too many warnings. So what are atoms 981 and 982? Does their motion look different in an important ways between the 4.0.7 and 4.5.4 trajectories? Chris. -- original message -- Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote: run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] GROMACS 4.5.4 keep crashing all the time
Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic may be different. It's important to rule out different variables to arrive at a solution, which I suspect is of interest to you. You also haven't addressed points #1 and #6 in Chris' message. -Justin Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000 LINCS, but this is usually a sign that something bad is going on in the system. OK. Chris suggested a number of other strategies that will help determine which aspect of 4.5.4 is behaving differently. How did those strategies work out? Mark Cheers, Itamar On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote: OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just water or remove the ions, etc? 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 4.5.4. Do you get the same lincs warnings? 6. Also, note that you are getting warnings and the run does not actually crash but just stops after too many warnings. So what are atoms 981 and 982? Does their motion look different in an important ways between the 4.0.7 and 4.5.4 trajectories? Chris. -- original message -- Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote: run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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/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] GROMACS 4.5.4 keep crashing all the time
Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find. Itamar On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote: Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic may be different. It's important to rule out different variables to arrive at a solution, which I suspect is of interest to you. You also haven't addressed points #1 and #6 in Chris' message. -Justin Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000 LINCS, but this is usually a sign that something bad is going on in the system. OK. Chris suggested a number of other strategies that will help determine which aspect of 4.5.4 is behaving differently. How did those strategies work out? Mark Cheers, Itamar On 18/08/2011, at 12:03 PM, chris.ne...@utoronto.ca wrote: OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just water or remove the ions, etc? 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 4.5.4. Do you get the same lincs warnings? 6. Also, note that you are getting warnings and the run does not actually crash but just stops after too many warnings. So what are atoms 981 and 982? Does their motion look different in an important ways between the 4.0.7 and 4.5.4 trajectories? Chris. -- original message -- Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote: run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time
HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much. It is just the fact that I am trying to give as much info as I can and to go over any idea in the mailing list without actually delay my other stuff. So again, I wish thanks for anyone who is helps here. On 01/09/2011, at 12:20 PM, chris.ne...@utoronto.ca wrote: Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers or by ruling out possibilities. It is actually useful information to know that Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others ... but when it seems like you don't want to provide the requested information my first inclination is to give up on trying to help. At this point, there are a few unanswered old questions and I have some new questions. 1. Can you reproduce this with a water box? The error is reproducible in a box of protein and water only. 2. Can you reproduce this with your protein in vacuum? The error is reproduced in vacuum. 3. If neither 2 or 3, then can you step slowly from one of these systems toward your final system and identify the point at which the lincs warnings arise? 4. Do you get the warnings without Ca also, or just with Ca? I am not sure what this mean. I get this warning mainly for N-H, but also for Ca-C, pairs of atoms 5. Can you reproduce this with the SD integrator? If you are really against trying this, then at least can you reproduce this with a single Berendsen temperature coupling group? When I use SD integrator, the simulations run fine. 6. Can you reproduce this without using the reaction field? Either with PME or a simple cutoff? Using PME the system is running just fine. 7. Can you trace down the version of gromacs (between 4.0.7 and 4.5.4) where you start to see this warning? I can't tell, 'cause I jump from 4.0.7 to 4.5.4. Thanks for the help, Itamar Chris. -- original message -- Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find. Itamar On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote: Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic may be different. It's important to rule out different variables to arrive at a solution, which I suspect is of interest to you. You also haven't addressed points #1 and #6 in Chris' message. -Justin Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000 LINCS, but this is usually a sign that something bad is going on in the system. OK. Chris suggested a number of other strategies that will help determine which aspect of 4.5.4 is behaving differently. How did those strategies work out? Mark Cheers, Itamar On 18/08/2011, at 12:03 PM, chris.neale at utoronto.ca wrote: OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just water or remove the ions, etc? 5. Take the output .gro from 4.0.7 that ran fine for X ns and run it under 4.5.4. Do you get the same lincs warnings? 6. Also, note that you are getting warnings and the run does not actually crash but just stops after too many warnings. So what are atoms 981 and 982? Does their motion look different in an important ways between the 4.0.7 and 4.5.4 trajectories? Chris. -- original message -- Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote: run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
Hi Itamar, In my experience, the 4.5 series appears to be slightly less tolerant of unstable systems than the 4.0 series. Try minimizing and/or equilibrating your system longer. See http://www.gromacs.org/Documentation/Errors and http://www.gromacs.org/Documentation/Terminology/Blowing_Up MZ On Wed, Aug 17, 2011 at 7:16 PM, Itamar Kass (Med) itamar.k...@monash.edu wrote: Hi Matthew, Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled by me (on my machine) or by the sys-admin on Linux cluster or blue-gene. The simulations using 4.5.4 crashed giving LINCS error, which is not the case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled with me (on my machine) or by the sys-admin on Linux cluster/blue-gene. cheers, Itamar -- 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] GROMACS 4.5.4 keep crashing all the time.
My apologies; the remainder of the thread in which these suggestions were already proposed and discussed showed up where I didn't expect them. Sorry to repeat what's already been said. MZ On Thu, Aug 18, 2011 at 12:58 PM, Matthew Zwier mczw...@gmail.com wrote: Hi Itamar, In my experience, the 4.5 series appears to be slightly less tolerant of unstable systems than the 4.0 series. Try minimizing and/or equilibrating your system longer. See http://www.gromacs.org/Documentation/Errors and http://www.gromacs.org/Documentation/Terminology/Blowing_Up MZ On Wed, Aug 17, 2011 at 7:16 PM, Itamar Kass (Med) itamar.k...@monash.edu wrote: Hi Matthew, Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled by me (on my machine) or by the sys-admin on Linux cluster or blue-gene. The simulations using 4.5.4 crashed giving LINCS error, which is not the case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled with me (on my machine) or by the sys-admin on Linux cluster/blue-gene. cheers, Itamar -- 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] GROMACS 4.5.4 keep crashing all the time.
Could be a system blowing up, or perhaps a mis-compiled binary. What error messages do you get when the crash occurs? On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass itamar.k...@monash.edu wrote: Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order to do so, I had used version 4.5.4. I had solvate the protein in water, add ions to naturalise the systems, equilibrated the systems and then tried productive runs. Now, no matter what I did, it crashed after few ps's of free MD or during the PR runs. Few of the things I had tried are: 1. Running the simulations on different systems (OSX, linux or blue-gene). 2. Using single or double precision versions. 3. An equilibration stage, 1ns long with a time-step of 1fs, during which the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 nm-2. 4. Running part of the equilibration stage as NVT and then switched to NPT. 5. Started from different x-ray structures, with resolutions differ from 2.5 to 1.7 Angstrom. Finally I had moved back to 4.0.7 which worked like charm. I wonder if someone else had encounter something like this. Attached please find the mdp files I used. All the best, Itamar. - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
Hi Matthew, Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled by me (on my machine) or by the sys-admin on Linux cluster or blue-gene. The simulations using 4.5.4 crashed giving LINCS error, which is not the case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled with me (on my machine) or by the sys-admin on Linux cluster/blue-gene. cheers, Itamar On 18 August 2011 01:48, Matthew Zwier mczw...@gmail.com wrote: Could be a system blowing up, or perhaps a mis-compiled binary. What error messages do you get when the crash occurs? On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass itamar.k...@monash.edu wrote: Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order to do so, I had used version 4.5.4. I had solvate the protein in water, add ions to naturalise the systems, equilibrated the systems and then tried productive runs. Now, no matter what I did, it crashed after few ps's of free MD or during the PR runs. Few of the things I had tried are: 1. Running the simulations on different systems (OSX, linux or blue-gene). 2. Using single or double precision versions. 3. An equilibration stage, 1ns long with a time-step of 1fs, during which the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 nm-2. 4. Running part of the equilibration stage as NVT and then switched to NPT. 5. Started from different x-ray structures, with resolutions differ from 2.5 to 1.7 Angstrom. Finally I had moved back to 4.0.7 which worked like charm. I wonder if someone else had encounter something like this. Attached please find the mdp files I used. All the best, Itamar. - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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 -- -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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: Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
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Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages I'd also add that we need a detailed description of the system, including force field used and any other special considerations (distance restraints, modified parameters, etc). An .mdp file would also be useful for the run that crashes. -Justin Do this for 4.0.7 and 4.5.4, for which I trust that you have been using exactly identical test systems. If not, then please try it again while conserving the system. Chris. -- original message -- Hi Matthew, Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled by me (on my machine) or by the sys-admin on Linux cluster or blue-gene. The simulations using 4.5.4 crashed giving LINCS error, which is not the case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled with me (on my machine) or by the sys-admin on Linux cluster/blue-gene. cheers, Itamar On 18 August 2011 01:48, Matthew Zwier mczwier at gmail.com wrote: Could be a system blowing up, or perhaps a mis-compiled binary. What error messages do you get when the crash occurs? On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass itamar.kass at monash.edu wrote: Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order to do so, I had used version 4.5.4. I had solvate the protein in water, add ions to naturalise the systems, equilibrated the systems and then tried productive runs. Now, no matter what I did, it crashed after few ps's of free MD or during the PR runs. Few of the things I had tried are: 1. Running the simulations on different systems (OSX, linux or blue-gene). 2. Using single or double precision versions. 3. An equilibration stage, 1ns long with a time-step of 1fs, during which the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 nm-2. 4. Running part of the equilibration stage as NVT and then switched to NPT. 5. Started from different x-ray structures, with resolutions differ from 2.5 to 1.7 Angstrom. Finally I had moved back to 4.0.7 which worked like charm. I wonder if someone else had encounter something like this. Attached please find the mdp files I used. All the best, Itamar. -- 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/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] GROMACS 4.5.4 keep crashing all the time.
Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 1 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro The em.mdp: integrator = steep maximum number of steps to integrate nsteps = 5 ;Energy minimizing stuff emstep = 0.001 emtol= 100.0 ; OPTIONS FOR BONDS constraints = none ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; Energy monitoring energygrps = system ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist= 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-rf = 62 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Center of mass control nstcomm = 1000 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode= linear ; Groups for center of mass motion removal comm-grps= system the pr.mdp: define = -DPOSRES integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100ps. ; OPTIONS FOR BONDS ; Constrain control constraints = all-bonds ; Do not constrain the start configuration continuation = no ; Type of constraint algorithm constraint-algorithm = lincs ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout = 10 nstfout = 10 ; Output frequency and precision for xtc file nstxtcout= 5000 xtc-precision= 1000 ; Energy monitoring energygrps = Protein Non-protein nstenergy= 5000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist= 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62; As suggested at J Comput Chem. 2004 Oct;25(13):1656-76. vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = Protein Non-Protein tau-t= 0.1 0.1 ref-t= 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; Generate velocites is on at 290K - do not get velocity from gro file. gen_vel = yes gen_temp= 290 gen-seed= -1 ; Center of mass control nstcomm = 1000 ;
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
On 18/08/2011 10:14 AM, Itamar Kass wrote: Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca mailto:chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 1 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro So you're doing solvated EM, then position-restrained NPT MD, then NPT. Sounds to me like you might have a bad initial contact that can't relax under solvated EM, nor under PR-NPT, and is getting numerically lucky in 4.0.7 and not under 4.5.4. If so, then careful inspection of the start of the 4.0.7 run might show this. Vacuo EM of the solute might help if the problem is intra-solute. Have you explored the suggestions here? http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.
I concur with what Mark suggested about in vacuo EM. I would also point out the following problem(s): and the md.mdp: Here you call for 300 K as the reference temperature and the temperature at which you've equilibrated: tc-grps = Protein Non-Protein tau-t= 0.1 0.1 ref-t= 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 290K - do not get velocity from gro file. And here you're destroying the previous equilibration by re-generating velocities and simultaneously generating velocities for the wrong temperature, which may or may not induce instability into the system. gen_vel = yes gen_temp= 290 gen-seed= -1 -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/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] GROMACS 4.5.4 keep crashing all the time.
Dear Mark, We also tried to minimise the system in vacuum before adding water and ions withou, but it still crashed when we did MD. Itamar. On 18/08/2011, at 10:31 AM, Mark Abraham wrote: On 18/08/2011 10:14 AM, Itamar Kass wrote: Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 1 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro So you're doing solvated EM, then position-restrained NPT MD, then NPT. Sounds to me like you might have a bad initial contact that can't relax under solvated EM, nor under PR-NPT, and is getting numerically lucky in 4.0.7 and not under 4.5.4. If so, then careful inspection of the start of the 4.0.7 run might show this. Vacuo EM of the solute might help if the problem is intra-solute. Have you explored the suggestions here? http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] GROMACS 4.5.4 keep crashing all the time.
Hi Justing, I had reinitialised the systems after the PR run but I don't think this is the origin of the error. Because the system with the Ca crashed allways in the PR state, although the systems run with 4.0.7 done it fine. Best, Itamnar On 18/08/2011, at 10:39 AM, Justin A. Lemkul wrote: I concur with what Mark suggested about in vacuo EM. I would also point out the following problem(s): and the md.mdp: Here you call for 300 K as the reference temperature and the temperature at which you've equilibrated: tc-grps = Protein Non-Protein tau-t= 0.1 0.1 ref-t= 300 300 ; Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 290K - do not get velocity from gro file. And here you're destroying the previous equilibration by re-generating velocities and simultaneously generating velocities for the wrong temperature, which may or may not induce instability into the system. gen_vel = yes gen_temp= 290 gen-seed= -1 -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/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 - In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] GROMACS 4.5.4 keep crashing all the time
Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.ne...@utoronto.ca wrote: run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.neale at utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages The command I had used (for both 4.0.7 and 4.5.4) are: pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5 grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname CL- -np 17 -seed 66 grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g 1EXR_em.log -c 1EXR_em.gro grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e 1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr mpirun mdrun_d_mpi -v -stepout 1 -s md.tpr -x 1EXR_md.xtc -e 1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro The em.mdp: integrator = steep maximum number of steps to integrate nsteps = 5 ;Energy minimizing stuff emstep = 0.001 emtol= 100.0 ; OPTIONS FOR BONDS constraints = none ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; Energy monitoring energygrps = system ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns-type = Grid ; nblist cut-off rlist= 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-rf = 62 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Center of mass control nstcomm = 1000 ; Periodic boundary conditions pbc = xyz ; Mode for center of mass motion removal comm-mode= linear ; Groups for center of mass motion removal comm-grps= system the pr.mdp: define = -DPOSRES integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100ps. ; OPTIONS FOR BONDS ; Constrain control constraints= all-bonds ; Do not constrain the start configuration continuation = no ; Type of constraint algorithm constraint-algorithm = lincs ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout= 10 nstfout= 10 ; Output frequency and precision for xtc file nstxtcout = 5000 xtc-precision = 1000 ; Energy monitoring energygrps = Protein Non-protein nstenergy = 5000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist= 5 ; ns algorithm (simple or grid) ns-type= Grid ; nblist cut-off rlist = 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62; As suggested at J Comput Chem. 2004 Oct;25(13):1656-76. vdw-type = Cut-off ; cut-off lengths rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = Protein Non-Protein tau-t= 0.1 0.1 ref-t= 300 300 ; Pressure
