Re: [gmx-users] Validation of molecular dynamic simulation results
Dear Ananya, Shouldn't this be something you already had in mind even before attempting to simulate? Usually, a simulation is a means to an end. What is your end, ie. what made you do this simulation? The motivation behind your simulation is usually what will determine what type of validation it requires. Sure, there are quasi-standard analysis and sanity checks that one almost always uses to ensure the simulation is relevant, but you can find those in any given MD tutorial available online. For this, Google is your friend and you also have quite popular tutorials such as Justin's for example: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ I suggest you sit down and think a bit about what are you attempting to achieve with your simulation. Pinpoint what type of analysis you need and then take a careful look at the Gromacs manual. There you will find all you need to know about the analysis tools available to you. They're not guaranteed to cover all your needs, but they usually more than suffice in providing what most researchers need to validate their simulations. Best regards, João On Tue, Feb 11, 2014 at 8:02 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hello everyone, I have done a set of molecular dynamic simulation of my protein and its mutated structure, now please tell me how should I validate the simulation results or structures. Whether I can reproduce the same simulations. Thank you in advance -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Validation of molecular dynamic simulation results
On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote: Dear Ananya, Shouldn't this be something you already had in mind even before attempting to simulate? Usually, a simulation is a means to an end. What is your end, ie. what made you do this simulation? The motivation behind your simulation is usually what will determine what type of validation it requires. Sure, there are quasi-standard analysis and sanity checks that one almost always uses to ensure the simulation is relevant, but you can find those in any given MD tutorial available online. For this, Google is your friend and you also have quite popular tutorials such as Justin's for example: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ I suggest you sit down and think a bit about what are you attempting to achieve with your simulation. Pinpoint what type of analysis you need and then take a careful look at the Gromacs manual. There you will find all you need to know about the analysis tools available to you. They're not guaranteed to cover all your needs, but they usually more than suffice in providing what most researchers need to validate their simulations. Best regards, João On Tue, Feb 11, 2014 at 8:02 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hello everyone, I have done a set of molecular dynamic simulation of my protein and its mutated structure, now please tell me how should I validate the simulation results or structures. Whether I can reproduce the same simulations. Thank you in advance -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Dear João, Thank you for your reply, I was intended to seen the difference in molecular movement of my protein upon mutation. My protein is a GTPase protein and I have done simulation in presence of GTP, GDP and GDP+Pi for both the wild type and the mutated protein. Then I have done principle component analysis and RMSD RMSF comparison of the trajectories. Now I want to check the authenticity of the set of simulation and whether they can be reproduce to validate my results. Please kindly help me in this regard. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Validation of molecular dynamic simulation results
Dear Ananya, Sorry but I don't understand what you're saying. What do you mean by molecular movement of my protein? Do you mean diffusion? Please be more specific. You also mention authenticity, but I don't think that's what you meant... You have done PCA, RMSD and RMSF analyses. That's nice and all, but do you have a reason for doing them? What I meant with my previous email is that *there is no fixed recipe that one must always follow in order to validate their simulations*. The analyses your simulation requires in order to be validated depend on the simulation purpose and what experimental data you have to compare them to. Take this overly simplistic example: Imagine I've performed a simple protein in water MD simulation. The protein is well behaved (stable native structure) and there is a high resolution experimental structure of it. Radius of gyration, RMSD, RMSF and DSSP analyses would be good candidates to show whether my force field, settings and parameters are adequate or not in maintaining the well known native 3D structure. Like I said before, you're the one that must be familiar with your system, simulation and overall project aim. I am happy to help you in identifying the tool you need to perform a certain analysis/study or even helping understanding any error or problem with it. However I cannot do your own work in identifying what needs to be done and where you're heading. Best regards, João On Tue, Feb 11, 2014 at 9:46 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote: Dear Ananya, Shouldn't this be something you already had in mind even before attempting to simulate? Usually, a simulation is a means to an end. What is your end, ie. what made you do this simulation? The motivation behind your simulation is usually what will determine what type of validation it requires. Sure, there are quasi-standard analysis and sanity checks that one almost always uses to ensure the simulation is relevant, but you can find those in any given MD tutorial available online. For this, Google is your friend and you also have quite popular tutorials such as Justin's for example: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ I suggest you sit down and think a bit about what are you attempting to achieve with your simulation. Pinpoint what type of analysis you need and then take a careful look at the Gromacs manual. There you will find all you need to know about the analysis tools available to you. They're not guaranteed to cover all your needs, but they usually more than suffice in providing what most researchers need to validate their simulations. Best regards, João On Tue, Feb 11, 2014 at 8:02 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hello everyone, I have done a set of molecular dynamic simulation of my protein and its mutated structure, now please tell me how should I validate the simulation results or structures. Whether I can reproduce the same simulations. Thank you in advance -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Dear João, Thank you for your reply, I was intended to seen the difference in molecular movement of my protein upon mutation. My protein is a GTPase protein and I have done simulation in presence of GTP, GDP and GDP+Pi for both the wild type and the mutated protein. Then I have done principle component analysis and RMSD RMSF comparison of the trajectories. Now I want to check the authenticity of the set of simulation and whether they can be reproduce to validate my results. Please kindly help me in this regard. -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Justifying 4fs production runs after 1fs equilibrations?
Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but does not use GROMACS. We have been developing protocol for these MD simulations, but we had some different views on equilibration and production. Equlibration My friend is recommending that I do equilibration for 500ps @ 1fs with no constraints. I have no real objection to that, but he made it seem like the results might be quite different than an equilibration for 200ps @ 2fs with LINCS all-bonds. Would it make a critical difference? Production I was excited by the performance possible with LINCS all-bonds, -vsite aromatics @ 4fs, but my friend looks at 4fs with disgust. I responded with arguments from the GROMACS 4 paper, and a paper called Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems re: the relationship between the period of the fastest vibration and largest allowable timestep, but he seems quite convinced that for publication, only 1fs and possibly 2fs production runs (preferably without barostat and thermostat??) are acceptable. The suggestion to drop the barostat and thermostat for production follows the philosophy that if your minimization and equilibration is properly done, then the system should be stable in production without pressure temperature control. I'm having a hard time finding better literature justifications for usage of LINCS all-bonds @ 2fs, and certainly for -vsites @ 4fs; PT control seems quite standard in publications using GROMACS. Can you suggest any papers or calculations I can do to show the validity of these options? -- View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Validation of molecular dynamic simulation results
Dear Sir, My protein contains two domain and upon GTP hydrolysis, the protein under goes conformational change and it shows inter-domain movement. I did few biochemical test which showed me that the upon a mutation in the conserved residue (which is localed in the chain connecting the two domain)the GTPase activity is reduced and also it has effected the cell growth. Now to see whether the mutation is some how effecting the inter domain movement of the protein(which is a important property of the protein for it function) I performed the simulations keeping the parameters close to the biochemical experiments(like con. of ions, temp. etc) . Now when I presented my work in a conference people asked me about its authenticity, how much close it is to the reality and whether it is reproducible. I want to know how to verify my simulations. Thanks in advance On Tue, 11 Feb 2014 11:24:53 +0100, João Henriques wrote: Dear Ananya, Sorry but I don't understand what you're saying. What do you mean by molecular movement of my protein? Do you mean diffusion? Please be more specific. You also mention authenticity, but I don't think that's what you meant... You have done PCA, RMSD and RMSF analyses. That's nice and all, but do you have a reason for doing them? What I meant with my previous email is that *there is no fixed recipe that one must always follow in order to validate their simulations*. The analyses your simulation requires in order to be validated depend on the simulation purpose and what experimental data you have to compare them to. Take this overly simplistic example: Imagine I've performed a simple protein in water MD simulation. The protein is well behaved (stable native structure) and there is a high resolution experimental structure of it. Radius of gyration, RMSD, RMSF and DSSP analyses would be good candidates to show whether my force field, settings and parameters are adequate or not in maintaining the well known native 3D structure. Like I said before, you're the one that must be familiar with your system, simulation and overall project aim. I am happy to help you in identifying the tool you need to perform a certain analysis/study or even helping understanding any error or problem with it. However I cannot do your own work in identifying what needs to be done and where you're heading. Best regards, João On Tue, Feb 11, 2014 at 9:46 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote: Dear Ananya, Shouldn't this be something you already had in mind even before attempting to simulate? Usually, a simulation is a means to an end. What is your end, ie. what made you do this simulation? The motivation behind your simulation is usually what will determine what type of validation it requires. Sure, there are quasi-standard analysis and sanity checks that one almost always uses to ensure the simulation is relevant, but you can find those in any given MD tutorial available online. For this, Google is your friend and you also have quite popular tutorials such as Justin's for example: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ I suggest you sit down and think a bit about what are you attempting to achieve with your simulation. Pinpoint what type of analysis you need and then take a careful look at the Gromacs manual. There you will find all you need to know about the analysis tools available to you. They're not guaranteed to cover all your needs, but they usually more than suffice in providing what most researchers need to validate their simulations. Best regards, João On Tue, Feb 11, 2014 at 8:02 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hello everyone, I have done a set of molecular dynamic simulation of my protein and its mutated structure, now please tell me how should I validate the simulation results or structures. Whether I can reproduce the same simulations. Thank you in advance -- Ananya Chatterjee, Senior Research Fellow (SRF), Department of biological Science, IISER-Kolkata. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Dear João, Thank you for your reply, I was intended to seen the difference in molecular movement of my protein upon mutation. My protein is a GTPase protein and I have done simulation in presence of GTP, GDP and GDP+Pi for both the wild type and the mutated protein. Then I have done principle component analysis and RMSD RMSF comparison of the trajectories. Now I want to check the authenticity of the set of simulation and whether they can be reproduce to validate my results.
Re: [gmx-users] Validation of molecular dynamic simulation results
First of all, please address me in a casual manner, Sir makes me feel old and I'm just in my mid 20's :) Now I'll try to be as less verbose as I can, because I think there's a little communication issue here. Authenticity usually points out towards originality, something not copied, genuine. I knew you meant something different and thus my previous remark. You don't have to tell us the full story behind the study you're doing. This mailing list serves to help people with difficulties regarding the gromacs software package. Your difficulty lies elsewhere, ie. you want someone to tell you what to do next in your project. *That is a scientific decision not a technical issue*, if you understand what I mean. It's something you have to discuss with your research group and collaborators. Unless you come to me with a concrete idea for an analysis/study I'm afraid I can't help you. Don't take this personally, but I simply can not do your homework in full. *Come to me with a concrete idea like, I want to measure how dissimilar A and B are or I want to know how I can compute this and that, etc, and then I (or someone else) might be able to assist you.* Best regards, João On Tue, Feb 11, 2014 at 12:43 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Dear Sir, My protein contains two domain and upon GTP hydrolysis, the protein under goes conformational change and it shows inter-domain movement. I did few biochemical test which showed me that the upon a mutation in the conserved residue (which is localed in the chain connecting the two domain)the GTPase activity is reduced and also it has effected the cell growth. Now to see whether the mutation is some how effecting the inter domain movement of the protein(which is a important property of the protein for it function) I performed the simulations keeping the parameters close to the biochemical experiments(like con. of ions, temp. etc) . Now when I presented my work in a conference people asked me about its authenticity, how much close it is to the reality and whether it is reproducible. I want to know how to verify my simulations. Thanks in advance On Tue, 11 Feb 2014 11:24:53 +0100, João Henriques wrote: Dear Ananya, Sorry but I don't understand what you're saying. What do you mean by molecular movement of my protein? Do you mean diffusion? Please be more specific. You also mention authenticity, but I don't think that's what you meant... You have done PCA, RMSD and RMSF analyses. That's nice and all, but do you have a reason for doing them? What I meant with my previous email is that *there is no fixed recipe that one must always follow in order to validate their simulations*. The analyses your simulation requires in order to be validated depend on the simulation purpose and what experimental data you have to compare them to. Take this overly simplistic example: Imagine I've performed a simple protein in water MD simulation. The protein is well behaved (stable native structure) and there is a high resolution experimental structure of it. Radius of gyration, RMSD, RMSF and DSSP analyses would be good candidates to show whether my force field, settings and parameters are adequate or not in maintaining the well known native 3D structure. Like I said before, you're the one that must be familiar with your system, simulation and overall project aim. I am happy to help you in identifying the tool you need to perform a certain analysis/study or even helping understanding any error or problem with it. However I cannot do your own work in identifying what needs to be done and where you're heading. Best regards, João On Tue, Feb 11, 2014 at 9:46 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote: Dear Ananya, Shouldn't this be something you already had in mind even before attempting to simulate? Usually, a simulation is a means to an end. What is your end, ie. what made you do this simulation? The motivation behind your simulation is usually what will determine what type of validation it requires. Sure, there are quasi-standard analysis and sanity checks that one almost always uses to ensure the simulation is relevant, but you can find those in any given MD tutorial available online. For this, Google is your friend and you also have quite popular tutorials such as Justin's for example: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ I suggest you sit down and think a bit about what are you attempting to achieve with your simulation. Pinpoint what type of analysis you need and then take a careful look at the Gromacs manual. There you will find all you need to know about the analysis tools available to you. They're not guaranteed to cover all your needs, but they usually more than suffice in providing what most researchers need to validate their simulations. Best regards, João
Re: [gmx-users] gromacs 4.6.4 query
On Tue, Feb 11, 2014 at 6:12 AM, Chaitali Chandratre chaitujo...@gmail.com wrote: Dear Sir, Below is error message for gromacs-4.6.4 gpu enabled install: --- make error : [chaitalij@gpu4 build-gpu]$ make [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o /opt/CUDA-5.5/include/host_config.h(72): catastrophic error: #error directive: -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is supported! #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is supported! ^ The error is right there, explained quite clearly in the above message. What you can do is to: - complain to NVIDIA AND - remove the limitation which is mostly a safety measure (AFAIK the nvcc + icc 13 is not fully tested and/or compatible) by either editing the above mentioned header or if you can't do that (no root access) creating a copy of to edit it and appending its path in CUDA_NVCC_FLAGS (i.e. adding ;-I/path/to/my/cuda-host-config-h). OR - use another compiler, e.g. gcc 4.8 will probably be faster than icc 13. CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating path/to/gromacs/gromacs-4.6.4/build-gpu/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 - Below is config command : -- /path/to/cmake-2.8.12.1/bin/cmake -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=/path/to//mkl/lib/intel64 -DMKL_INCLUDE_DIR=/path/to//mkl/include -D CMAKE_INSTALL_PREFIX=/path/to//gromacs-4.6.4/build-gpu/ -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_HOST_COMPILER=/path/to/intel64/icc -DCUDA_TOOLKIT_ROOT_DIR=/opt/CUDA-5.5/ /path/to/gromacs-4.6.4/ Icc details : icc version 13.0.1 (gcc version 4.4.6 compatibility) OpenMM is not available in environment. On Mon, Feb 10, 2014 at 6:15 PM, Szilárd Páll pall.szil...@gmail.comwrote: On Mon, Feb 10, 2014 at 1:27 PM, Chaitali Chandratre chaitujo...@gmail.com wrote: Dear Sir, I have question w.r.t gromacs-4.6.4 installation with GPU support. I have installed non-GPU vesion(for 4.6.4) and it works fine. But while compiling with gpu (-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/CUDA-5.5) It gives compilation error. The node is having gpu card fermi and cuda5.5. Do I need to set some more things? Yes, perhaps you could tell us what the error is. :) -- Szilárd Thanks. -- With Regards, Chaitali I know everything happens for a reason...But sometimes I wish I knew what the reason was !! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- With Regards, Chaitali I know everything happens for a reason...But sometimes I wish I knew what the reason was !! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations?
On Tue, Feb 11, 2014 at 12:11 PM, unitALX alec.zan...@gmail.com wrote: Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but does not use GROMACS. We have been developing protocol for these MD simulations, but we had some different views on equilibration and production. Equlibration My friend is recommending that I do equilibration for 500ps @ 1fs with no constraints. I have no real objection to that, but he made it seem like the results might be quite different than an equilibration for 200ps @ 2fs with LINCS all-bonds. Would it make a critical difference? Production I was excited by the performance possible with LINCS all-bonds, -vsite aromatics @ 4fs, but my friend looks at 4fs with disgust. I would you mind asking your friend whether multiple time stepping disgusts him too? :) -- Szilárd I responded with arguments from the GROMACS 4 paper, and a paper called Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems re: the relationship between the period of the fastest vibration and largest allowable timestep, but he seems quite convinced that for publication, only 1fs and possibly 2fs production runs (preferably without barostat and thermostat??) are acceptable. The suggestion to drop the barostat and thermostat for production follows the philosophy that if your minimization and equilibration is properly done, then the system should be stable in production without pressure temperature control. I'm having a hard time finding better literature justifications for usage of LINCS all-bonds @ 2fs, and certainly for -vsites @ 4fs; PT control seems quite standard in publications using GROMACS. Can you suggest any papers or calculations I can do to show the validity of these options? -- View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] AMBER03 force field for protein-ligand complex
hi GMX users i want to use AMBER03 force field for protein-ligand complex simulation. can i use antechamber for the particle charges of the ligand or i must to use b3lyp/cc-pVTZ calculation in an implicit solvent model? thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Validation of molecular dynamic simulation results
Hi Ananya, You have several options to validate the results you have 1. Perform the simulations again 2. Apply the reverse mutations and simulate again 3. Perform (covariance) analysis on different blocks 4. Extract a measurable property and compare it to experiments ad 1.: Redoing the simulations is pretty trivial. Just set different initial velocities, different random placement of ions. If the results end up the same, that gives confidence that your approach is solid. ad 2.: If the effect you see is due to the mutation, then reversing the mutation should bring you in the opposite direction again. ad 3.: If you've reached an equilibrium situation, then your principal components will end up the same AND the mean projections per window will be approximately equal. ad 4.: If there's anything known about NOEs obtained from NMR or the hydrodynamic radius or something else from experiments, you can derive related properties from your simulations and compare these (qualitatively, probably). Hope it helps, Tsjerk On Tue, Feb 11, 2014 at 1:38 PM, João Henriques joao.henriques.32...@gmail.com wrote: First of all, please address me in a casual manner, Sir makes me feel old and I'm just in my mid 20's :) Now I'll try to be as less verbose as I can, because I think there's a little communication issue here. Authenticity usually points out towards originality, something not copied, genuine. I knew you meant something different and thus my previous remark. You don't have to tell us the full story behind the study you're doing. This mailing list serves to help people with difficulties regarding the gromacs software package. Your difficulty lies elsewhere, ie. you want someone to tell you what to do next in your project. *That is a scientific decision not a technical issue*, if you understand what I mean. It's something you have to discuss with your research group and collaborators. Unless you come to me with a concrete idea for an analysis/study I'm afraid I can't help you. Don't take this personally, but I simply can not do your homework in full. *Come to me with a concrete idea like, I want to measure how dissimilar A and B are or I want to know how I can compute this and that, etc, and then I (or someone else) might be able to assist you.* Best regards, João On Tue, Feb 11, 2014 at 12:43 PM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Dear Sir, My protein contains two domain and upon GTP hydrolysis, the protein under goes conformational change and it shows inter-domain movement. I did few biochemical test which showed me that the upon a mutation in the conserved residue (which is localed in the chain connecting the two domain)the GTPase activity is reduced and also it has effected the cell growth. Now to see whether the mutation is some how effecting the inter domain movement of the protein(which is a important property of the protein for it function) I performed the simulations keeping the parameters close to the biochemical experiments(like con. of ions, temp. etc) . Now when I presented my work in a conference people asked me about its authenticity, how much close it is to the reality and whether it is reproducible. I want to know how to verify my simulations. Thanks in advance On Tue, 11 Feb 2014 11:24:53 +0100, João Henriques wrote: Dear Ananya, Sorry but I don't understand what you're saying. What do you mean by molecular movement of my protein? Do you mean diffusion? Please be more specific. You also mention authenticity, but I don't think that's what you meant... You have done PCA, RMSD and RMSF analyses. That's nice and all, but do you have a reason for doing them? What I meant with my previous email is that *there is no fixed recipe that one must always follow in order to validate their simulations*. The analyses your simulation requires in order to be validated depend on the simulation purpose and what experimental data you have to compare them to. Take this overly simplistic example: Imagine I've performed a simple protein in water MD simulation. The protein is well behaved (stable native structure) and there is a high resolution experimental structure of it. Radius of gyration, RMSD, RMSF and DSSP analyses would be good candidates to show whether my force field, settings and parameters are adequate or not in maintaining the well known native 3D structure. Like I said before, you're the one that must be familiar with your system, simulation and overall project aim. I am happy to help you in identifying the tool you need to perform a certain analysis/study or even helping understanding any error or problem with it. However I cannot do your own work in identifying what needs to be done and where you're heading. Best regards, João On Tue, Feb 11, 2014 at 9:46 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote:
Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations?
Hehe that is a good point! Indeed, he says that multiple time stepping is a better compromise on increasing speed. However, he says the NAMD multiple step scheme uses 4fs for long range electrostatics, while using 1fs for bonded interactions. So actually, the theoretical root of the disagreement seems to be on the validity of using length constraints for all bonds. The gist of what he was saying is that moving to a larger global timestep could cause you to miss interactions, effectively skipping over small local minima, and deviate from sampling the real hypersurface. He seemed OK with fixing the length of heavy-atom to hydrogen bonds and doing production at 2fs, but not fixing heavy-to-heavy bond lengths. Virtual sites + global 4fs seems taboo. For the same protein, I have a workflow using LINCS all-bonds @ 2fs for equilibration and production, and a workflow using LINCS all-bonds + vsite aromatics @ 4fs for equilibration and production. What parameters should I show for comparison? On Tue, Feb 11, 2014 at 3:00 PM, Szilárd Páll-2 [via GROMACS] ml-node+s5086n5014465...@n6.nabble.com wrote: On Tue, Feb 11, 2014 at 12:11 PM, unitALX [hidden email]http://user/SendEmail.jtp?type=nodenode=5014465i=0 wrote: Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but does not use GROMACS. We have been developing protocol for these MD simulations, but we had some different views on equilibration and production. Equlibration My friend is recommending that I do equilibration for 500ps @ 1fs with no constraints. I have no real objection to that, but he made it seem like the results might be quite different than an equilibration for 200ps @ 2fs with LINCS all-bonds. Would it make a critical difference? Production I was excited by the performance possible with LINCS all-bonds, -vsite aromatics @ 4fs, but my friend looks at 4fs with disgust. I would you mind asking your friend whether multiple time stepping disgusts him too? :) -- Szilárd I responded with arguments from the GROMACS 4 paper, and a paper called Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems re: the relationship between the period of the fastest vibration and largest allowable timestep, but he seems quite convinced that for publication, only 1fs and possibly 2fs production runs (preferably without barostat and thermostat??) are acceptable. The suggestion to drop the barostat and thermostat for production follows the philosophy that if your minimization and equilibration is properly done, then the system should be stable in production without pressure temperature control. I'm having a hard time finding better literature justifications for usage of LINCS all-bonds @ 2fs, and certainly for -vsites @ 4fs; PT control seems quite standard in publications using GROMACS. Can you suggest any papers or calculations I can do to show the validity of these options? -- View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [hidden email]http://user/SendEmail.jtp?type=nodenode=5014465i=1. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [hidden email]http://user/SendEmail.jtp?type=nodenode=5014465i=2. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461p5014465.html To unsubscribe from Justifying 4fs production runs after 1fs equilibrations?, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5014461code=YWxlYy56YW5kZXJAZ21haWwuY29tfDUwMTQ0NjF8MTcxMDQ5NjUwOA== .
Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations?
Hi, Personally I would also ask your colleague if he could also provide evidence (e.g. published papers) to back up what he is saying to you (i.e. that it is necessary to use a 1 fs timestep with an NVE ensemble to achieve acceptable results). This way, you can make an informed decision based upon the available evidence you can find, rather than simply upon one persons view point. I would suggest the he will find it difficult to come up with such evidence for your case of a straight forward MD simulation. You should also remember that you are the one that will need to be able to defend (to an examiner or reviewer) what you have done and why. Simply because the postdoc told me it was the correct thing to do will (unfortunately) not be good enough! Cheers Tom From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Szilárd Páll [pall.szil...@gmail.com] Sent: 11 February 2014 13:33 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations? On Tue, Feb 11, 2014 at 12:11 PM, unitALX alec.zan...@gmail.com wrote: Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but does not use GROMACS. We have been developing protocol for these MD simulations, but we had some different views on equilibration and production. Equlibration My friend is recommending that I do equilibration for 500ps @ 1fs with no constraints. I have no real objection to that, but he made it seem like the results might be quite different than an equilibration for 200ps @ 2fs with LINCS all-bonds. Would it make a critical difference? Production I was excited by the performance possible with LINCS all-bonds, -vsite aromatics @ 4fs, but my friend looks at 4fs with disgust. I would you mind asking your friend whether multiple time stepping disgusts him too? :) -- Szilárd I responded with arguments from the GROMACS 4 paper, and a paper called Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems re: the relationship between the period of the fastest vibration and largest allowable timestep, but he seems quite convinced that for publication, only 1fs and possibly 2fs production runs (preferably without barostat and thermostat??) are acceptable. The suggestion to drop the barostat and thermostat for production follows the philosophy that if your minimization and equilibration is properly done, then the system should be stable in production without pressure temperature control. I'm having a hard time finding better literature justifications for usage of LINCS all-bonds @ 2fs, and certainly for -vsites @ 4fs; PT control seems quite standard in publications using GROMACS. Can you suggest any papers or calculations I can do to show the validity of these options? -- View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_enermat: group.dat file
Hello, I found the following posts in the forum related to g_enemat problems: (A) year 2001 post: http://gromacs.5086.x6.nabble.com/using-g-enemat-td4391042.html (B) year 2013 post: http://gromacs.5086.x6.nabble.com/interaction-energy-using-g-enemat-td5010085.html In this post, Justin mentions I think g_enemat is buggy. People post the same issue or slight variants of it all the time. My version 4.6 installation fares even worse, as group names aren't even recognized (set to 'null' for everything). You can get interaction energies over time using g_energy, but I don't think g_enemat currently functions properly. -Justin (C) There is another 2013 post: http://gromacs.5086.x6.nabble.com/Problem-in-g-enemat-in-Gromacs-4-5-5-td5009607.html The post (A) from 2001, will that work? or there is some issue related to g_enemat. Could you please guide Thanks, sxn On Mon, Feb 10, 2014 at 4:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/10/14, 3:59 PM, shivangi nangia wrote: Dear Gromacs users, I have a question regarding the input file group.dat that has to be supplied for using g_enemat. The manual says With *-groups* a file must be supplied with on each line a group to be used. I need to calculate the interaction energy of each of my protein residue (186 residues) with only tail groups of the bi-layer. I am not sure what exactly to write in the group.dat file: residue numbers? atom/bead (CG) name? Will it use the groups I had in the index file that were incorporated in the .edr file? What you need are energygrps in the .mdp file. g_enemat is only a post-processing tool for existing energygrps; it cannot decompose nonbonded interactions in the way that you want. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_enermat: group.dat file
On 2/11/14, 10:09 AM, shivangi nangia wrote: Hello, I found the following posts in the forum related to g_enemat problems: (A) year 2001 post: http://gromacs.5086.x6.nabble.com/using-g-enemat-td4391042.html (B) year 2013 post: http://gromacs.5086.x6.nabble.com/interaction-energy-using-g-enemat-td5010085.html In this post, Justin mentions I think g_enemat is buggy. People post the same issue or slight variants of it all the time. My version 4.6 installation fares even worse, as group names aren't even recognized (set to 'null' for everything). You can get interaction energies over time using g_energy, but I don't think g_enemat currently functions properly. -Justin (C) There is another 2013 post: http://gromacs.5086.x6.nabble.com/Problem-in-g-enemat-in-Gromacs-4-5-5-td5009607.html The post (A) from 2001, will that work? or there is some issue related to g_enemat. g_enemat should work in 4.6.5 or any 5.0-beta release. The bug was fixed: http://redmine.gromacs.org/issues/1312. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations?
Yar, I understand. However, because of the differences in software experience (NAMD / GROMACS), presenting literature references is not as effective as I thought it would be, historical inertia and spirited argumentation is having more weight than I thought it would, and in between what is published for GROMACS and his best practice methods for NAMD, there is a gray area for which is effectively being biased towards NAMD style protocols (or what have you) and while you are correct in the long-term thermodynamic limit of publishing work, I have kinetic barrier to overcome in explaining something to someone who has seniority over me in my place of work and whose advice gives the de facto direction of the work I do. Hence why I am asking this more gray question of how to justify and explain across the software divide what I think are faster but valid choices for protocols. It is with considerable uneasiness that I see explanations being made in this gray area that are not consistent with the papers I am reading. To be more blunt about my situation, we are in a gray area on the choice of a homology model whose stability is being assessed by dynamics, and I am hearing people say things like well its a gray area, we can just argue it this way, or that way, and then we'll submit the results to a journal, and if they don't agree, we'll just submit the same work to another journal. I face a higher burden of proof than the textbook approach. Please advise. On Tue, Feb 11, 2014 at 4:12 PM, TomPiggot [via GROMACS] ml-node+s5086n5014470...@n6.nabble.com wrote: Hi, Personally I would also ask your colleague if he could also provide evidence (e.g. published papers) to back up what he is saying to you (i.e. that it is necessary to use a 1 fs timestep with an NVE ensemble to achieve acceptable results). This way, you can make an informed decision based upon the available evidence you can find, rather than simply upon one persons view point. I would suggest the he will find it difficult to come up with such evidence for your case of a straight forward MD simulation. You should also remember that you are the one that will need to be able to defend (to an examiner or reviewer) what you have done and why. Simply because the postdoc told me it was the correct thing to do will (unfortunately) not be good enough! Cheers Tom From: [hidden email]http://user/SendEmail.jtp?type=nodenode=5014470i=0[[hidden email] http://user/SendEmail.jtp?type=nodenode=5014470i=1] on behalf of Szilárd Páll [[hidden email]http://user/SendEmail.jtp?type=nodenode=5014470i=2] Sent: 11 February 2014 13:33 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations? On Tue, Feb 11, 2014 at 12:11 PM, unitALX [hidden email]http://user/SendEmail.jtp?type=nodenode=5014470i=3 wrote: Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but does not use GROMACS. We have been developing protocol for these MD simulations, but we had some different views on equilibration and production. Equlibration My friend is recommending that I do equilibration for 500ps @ 1fs with no constraints. I have no real objection to that, but he made it seem like the results might be quite different than an equilibration for 200ps @ 2fs with LINCS all-bonds. Would it make a critical difference? Production I was excited by the performance possible with LINCS all-bonds, -vsite aromatics @ 4fs, but my friend looks at 4fs with disgust. I would you mind asking your friend whether multiple time stepping disgusts him too? :) -- Szilárd I responded with arguments from the GROMACS 4 paper, and a paper called Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems re: the relationship between the period of the fastest vibration and largest allowable timestep, but he seems quite convinced that for publication, only 1fs and possibly 2fs production runs (preferably without barostat and thermostat??) are acceptable. The suggestion to drop the barostat and thermostat for production follows the philosophy that if your minimization and equilibration is properly done, then the system should be stable in production without pressure temperature control. I'm having a hard time finding better literature justifications for usage of LINCS all-bonds @ 2fs, and certainly for -vsites @ 4fs; PT control seems quite standard in publications using GROMACS. Can you suggest any papers or calculations I can do to show the validity of these options? -- View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html
Re: [gmx-users] Validation of molecular dynamic simulation results
Well, I also would check which kind of movements I am looking for. It is a known fact that some domain (and, thereby, larger) movements occur in larger timescales and that might not be your case. E.g: you are expecting to see major movements in nanoseconds timescale. I hope this helps. Best regards, -- Marcelo Depólo Polêto Uppsala Universitet - Sweden -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Validation of molecular dynamic simulation results
On 2/11/14, 6:43 AM, ananyachatterjee wrote: Dear Sir, My protein contains two domain and upon GTP hydrolysis, the protein under goes conformational change and it shows inter-domain movement. I did few biochemical test which showed me that the upon a mutation in the conserved residue (which is localed in the chain connecting the two domain)the GTPase activity is reduced and also it has effected the cell growth. Now to see whether the mutation is some how effecting the inter domain movement of the protein(which is a important property of the protein for it function) I performed the simulations keeping the parameters close to the biochemical experiments(like con. of ions, temp. etc) . Now when I presented my work in a conference people asked me about its authenticity, how much close it is to the reality and whether it is reproducible. I want to know how to verify my simulations. Reproducibility is an important issue, especially in simulations. You should read the following page: http://www.gromacs.org/Documentation/Terminology/Reproducibility Related issues are convergence and sampling. If I had to guess, I would assume that's what the main criticism from the conference is. A single simulation may not be at all representative of reality; in fact, it may be an outlier of the real behavior. A simulation that is long enough such that the time average of the trajectory reflects the ensemble average is ergodic. That's hard to do and hard to prove, so typically multiple simulations are conducted and analyzed. If they all converge towards the same behavior, the outcome is much more reliable. Beyond that, there is no program that one can magically run to ensure that a simulation is valid or reliable. Correspondence with experimental observations is critical to making such arguments, though you haven't provided much concrete detail there in terms of what you can look at. -Justin Thanks in advance On Tue, 11 Feb 2014 11:24:53 +0100, João Henriques wrote: Dear Ananya, Sorry but I don't understand what you're saying. What do you mean by molecular movement of my protein? Do you mean diffusion? Please be more specific. You also mention authenticity, but I don't think that's what you meant... You have done PCA, RMSD and RMSF analyses. That's nice and all, but do you have a reason for doing them? What I meant with my previous email is that *there is no fixed recipe that one must always follow in order to validate their simulations*. The analyses your simulation requires in order to be validated depend on the simulation purpose and what experimental data you have to compare them to. Take this overly simplistic example: Imagine I've performed a simple protein in water MD simulation. The protein is well behaved (stable native structure) and there is a high resolution experimental structure of it. Radius of gyration, RMSD, RMSF and DSSP analyses would be good candidates to show whether my force field, settings and parameters are adequate or not in maintaining the well known native 3D structure. Like I said before, you're the one that must be familiar with your system, simulation and overall project aim. I am happy to help you in identifying the tool you need to perform a certain analysis/study or even helping understanding any error or problem with it. However I cannot do your own work in identifying what needs to be done and where you're heading. Best regards, João On Tue, Feb 11, 2014 at 9:46 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: On Tue, 11 Feb 2014 09:05:19 +0100, João Henriques wrote: Dear Ananya, Shouldn't this be something you already had in mind even before attempting to simulate? Usually, a simulation is a means to an end. What is your end, ie. what made you do this simulation? The motivation behind your simulation is usually what will determine what type of validation it requires. Sure, there are quasi-standard analysis and sanity checks that one almost always uses to ensure the simulation is relevant, but you can find those in any given MD tutorial available online. For this, Google is your friend and you also have quite popular tutorials such as Justin's for example: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ I suggest you sit down and think a bit about what are you attempting to achieve with your simulation. Pinpoint what type of analysis you need and then take a careful look at the Gromacs manual. There you will find all you need to know about the analysis tools available to you. They're not guaranteed to cover all your needs, but they usually more than suffice in providing what most researchers need to validate their simulations. Best regards, João On Tue, Feb 11, 2014 at 8:02 AM, ananyachatterjee ananyachatter...@iiserkol.ac.in wrote: Hello everyone, I have done a set of molecular dynamic simulation of my protein and its mutated structure, now please tell me how should I validate the simulation results
Re: [gmx-users] peptide aggregation
On 2/11/14, 1:59 PM, Shine A wrote: Hi, Now I am studying the aggregation propensity of a peptide using gromacs. To study the effect of neighbouring molecules on aggregation I am planning to do an MD simulation by reducing distance between end of the protein and edge of the box. Is this is physically significant? Then what is the optimum distance for that? Your intent is to use periodic images of the peptide to study its aggregation? By allowing the peptide to see itself, you've violating the minimum image convention. Such an approach is not sound. If you want to study aggregation, put multiple peptides in the box like everyone else does :) -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Protein - Ligand simulation
Hi, I'm not a Biologist, I'm designer interested to molecular modelling and 3D visualization of proteins and molcules. I use gromacs but I'm not an expert of this. I would create an animation of the interaction between D-Alanyl -D Alanine carboxypeptidase and penicillin. In general i would see how the penicillin attack the enzime that build bacterial's wall and I would see it in an animation that it will processed into a Graphic 3D software (like as Maya or Blender). I've a .pdb file of complex of the Streptomyces R61 DD-peptidase with penicillin G (pdb ID 1pwc). I would like to know if I can realize this trajectory with gromacs. I would have initially two separate molecules in a solvent and and see how these two molecules bind in an animation. Some of you could give me directions on how to get this trajectory? Thank you in advance. -- View this message in context: http://gromacs.5086.x6.nabble.com/Protein-Ligand-simulation-tp5014482.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein - Ligand simulation
You should take a look at this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html Best, Aldo === Aldo Segura-Cabrera Postdoctoral Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: aldo.segura-cabr...@cchmc.org; aldoseg...@gmail.com = El Martes, 11 de febrero, 2014 14:25:36, lucaam86 borrol...@gmail.com escribió: Hi, I'm not a Biologist, I'm designer interested to molecular modelling and 3D visualization of proteins and molcules. I use gromacs but I'm not an expert of this. I would create an animation of the interaction between D-Alanyl -D Alanine carboxypeptidase and penicillin. In general i would see how the penicillin attack the enzime that build bacterial's wall and I would see it in an animation that it will processed into a Graphic 3D software (like as Maya or Blender). I've a .pdb file of complex of the Streptomyces R61 DD-peptidase with penicillin G (pdb ID 1pwc). I would like to know if I can realize this trajectory with gromacs. I would have initially two separate molecules in a solvent and and see how these two molecules bind in an animation. Some of you could give me directions on how to get this trajectory? Thank you in advance. -- View this message in context: http://gromacs.5086.x6.nabble.com/Protein-Ligand-simulation-tp5014482.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations?
Hi, For your problem of assessing a homology model, I think that there are lots of other issues that I would be far more concerned about (e.g. force field accuracy, convergence of your simulations, etc.). To be fairly sure of anything I see in a simulation, I ideally would like to observe the same thing happening in a number of simulations using a number of different conditions, be that with different force fields, different starting structures, etc. I know that this is not always feasible but wherever possible I would try to do this. If you were to see different things with your different potential setups (4 fs with virtual sites and 2 fs constraining h-bonds or all-bonds), I would be more inclined to look for another issue (e.g. convergence) rather than these two different setup's. Regarding the issue of persuading the postdoc of your suggested approach, I cannot suggest more than you have been doing. If he is not willing to accept the evidence that you are showing him, the only thing you can do is to try and find more. There are plenty of papers out there that use the 4 fs and virtual sites setup. For what's its worth, I have used both types of setups for simulations of membranes (which have some explicit hydrogens, so not just united-atom PC membranes) and have seen no significant differences in the membrane properties using the two different approaches. Relating to your specific time step issue and publishing, as long as you can show that what you have done is sensible (such as through reading, following the advice of and referencing the paper and manual that you mentioned before), I cannot see how a manuscript would be rejected solely upon this matter. That might not be the case for some of the other things I have alluded to, such as being able to show convergence, reproducibility and so on. Anyway, these are just some of my personal opinions. Hopefully they help a little with your situation. I am sure that there are others on the list with more experience of such matters than me who can also help. Cheers Tom On 02/11/2014 03:45 PM, unitALX wrote: Yar, I understand. However, because of the differences in software experience (NAMD / GROMACS), presenting literature references is not as effective as I thought it would be, historical inertia and spirited argumentation is having more weight than I thought it would, and in between what is published for GROMACS and his best practice methods for NAMD, there is a gray area for which is effectively being biased towards NAMD style protocols (or what have you) and while you are correct in the long-term thermodynamic limit of publishing work, I have kinetic barrier to overcome in explaining something to someone who has seniority over me in my place of work and whose advice gives the de facto direction of the work I do. Hence why I am asking this more gray question of how to justify and explain across the software divide what I think are faster but valid choices for protocols. It is with considerable uneasiness that I see explanations being made in this gray area that are not consistent with the papers I am reading. To be more blunt about my situation, we are in a gray area on the choice of a homology model whose stability is being assessed by dynamics, and I am hearing people say things like well its a gray area, we can just argue it this way, or that way, and then we'll submit the results to a journal, and if they don't agree, we'll just submit the same work to another journal. I face a higher burden of proof than the textbook approach. Please advise. On Tue, Feb 11, 2014 at 4:12 PM, TomPiggot [via GROMACS] ml-node+s5086n5014470...@n6.nabble.com wrote: Hi, Personally I would also ask your colleague if he could also provide evidence (e.g. published papers) to back up what he is saying to you (i.e. that it is necessary to use a 1 fs timestep with an NVE ensemble to achieve acceptable results). This way, you can make an informed decision based upon the available evidence you can find, rather than simply upon one persons view point. I would suggest the he will find it difficult to come up with such evidence for your case of a straight forward MD simulation. You should also remember that you are the one that will need to be able to defend (to an examiner or reviewer) what you have done and why. Simply because the postdoc told me it was the correct thing to do will (unfortunately) not be good enough! Cheers Tom From: [hidden email]http://user/SendEmail.jtp?type=nodenode=5014470i=0[[hidden email] http://user/SendEmail.jtp?type=nodenode=5014470i=1] on behalf of Szilárd Páll [[hidden email]http://user/SendEmail.jtp?type=nodenode=5014470i=2] Sent: 11 February 2014 13:33 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations? On Tue, Feb 11, 2014 at 12:11 PM, unitALX [hidden
Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations?
On Tue, Feb 11, 2014 at 12:11 PM, unitALX alec.zan...@gmail.com wrote: Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but does not use GROMACS. We have been developing protocol for these MD simulations, but we had some different views on equilibration and production. Equlibration My friend is recommending that I do equilibration for 500ps @ 1fs with no constraints. I have no real objection to that, but he made it seem like the results might be quite different than an equilibration for 200ps @ 2fs with LINCS all-bonds. Would it make a critical difference? Highly unlikely. The point of equilibration is to move from some point near the ensemble, to some point in the ensemble, perhaps without perturbing the starting structure significantly. The last phase of equilibration should match the production ensemble (or simply be subtracted from the production run), but this is not likely to be critical, either. Production I was excited by the performance possible with LINCS all-bonds, -vsite aromatics @ 4fs, but my friend looks at 4fs with disgust. I responded with arguments from the GROMACS 4 paper, and a paper called Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems re: the relationship between the period of the fastest vibration and largest allowable timestep, but he seems quite convinced that for publication, only 1fs and possibly 2fs production runs (preferably without barostat and thermostat??) are acceptable. Historically, people used thermostats to cover up inadequacies in the model physics (e.g. no long-ranged electrostatics), but it was bad practice. If you can show energy conservation in the NVE version of the NPT/NVT/whatever ensemble you propose, then most of the issues are covered. IIRC there's a conserved quantity for these other ensembles too, but I'm not sure GROMACS reports it in all cases. Using NVE, 1fs (and maybe double precision) because historically that was the only observably rigorous ensemble implementation in code X is not a relevant argument now. The suggestion to drop the barostat and thermostat for production follows the philosophy that if your minimization and equilibration is properly done, then the system should be stable in production without pressure temperature control. Stable, yes. But stability is more of a precondition these days, not an objective ;-) In particular, if the conserved quantity gets conserved, then you can be pretty sure of stability. Sampling the right ensemble is the objective. The larger the system, the less the ensemble details matter. I'm having a hard time finding better literature justifications for usage of LINCS all-bonds @ 2fs, and certainly for -vsites @ 4fs; PT control seems quite standard in publications using GROMACS. Can you suggest any papers or calculations I can do to show the validity of these options? As Thomas has suggested, your simulation observables and their convergence are the relevant things to consider. Supposing that there are minima of relevant interactions seen at 1fs that are not seen at 4fs is all very well, but worth testing rather than assuming. Why are there not relevant minima seen at 0.5fs? ;-) The timescales of the system are relevant, and only experience and measurement can settle that. I would argue that I've always done it with 1fs and been happy is not a useful argument against conservative 4fs, unless there's also evidence of femto- second scale kinetics that matter. Also, if such a missed configuration is interesting, it will be seen if the ensemble converges, by definition. Worrying about it seems to give a lot of (undue?) weight to the order in which states are visited, and by implication the starting configuration... But since you are sampling in the unconverged limit of N time steps, one subset is not necessarily any better than another. It seems likely to me that a longer time step is more likely to access new areas of phase space when in the unconverged N-step limit; this is one reason for coarse-graining, of course. Mark -- View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab
Re: [gmx-users] Protein - Ligand simulation
On 2/11/14, 2:48 PM, Aldo Segura wrote: You should take a look at this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html It's worth noting that while what the OP is trying to can be accomplished using SMD, the time investment would be quite significant. Proper implementation of the pull code, coupled with selective restraints on the protein (hitting a moving target!), and parametrization of penicillin to be at least reasonably stable during the simulation all present challenges, especially for a non-specialist. -Justin Best, Aldo === Aldo Segura-Cabrera Postdoctoral Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: aldo.segura-cabr...@cchmc.org; aldoseg...@gmail.com = El Martes, 11 de febrero, 2014 14:25:36, lucaam86 borrol...@gmail.com escribió: Hi, I'm not a Biologist, I'm designer interested to molecular modelling and 3D visualization of proteins and molcules. I use gromacs but I'm not an expert of this. I would create an animation of the interaction between D-Alanyl -D Alanine carboxypeptidase and penicillin. In general i would see how the penicillin attack the enzime that build bacterial's wall and I would see it in an animation that it will processed into a Graphic 3D software (like as Maya or Blender). I've a .pdb file of complex of the Streptomyces R61 DD-peptidase with penicillin G (pdb ID 1pwc). I would like to know if I can realize this trajectory with gromacs. I would have initially two separate molecules in a solvent and and see how these two molecules bind in an animation. Some of you could give me directions on how to get this trajectory? Thank you in advance. -- View this message in context: http://gromacs.5086.x6.nabble.com/Protein-Ligand-simulation-tp5014482.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Hi Justin. I hope you have a nice day I would like to simulate a peptide on the membrane .In tutorial gromacs that simulate peptide KALP_15 in membrane DPPC ,you use inflate and shrink step.Do I need to do this step for my system? May you can help me؟ Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
