Re: [gmx-users] results of md
On 12/4/12 4:15 PM, mohammad agha wrote: Dear Justin, Thank you very much from your response. It means that this problem is not important. Should I use -reprod option in running of md.mdp? I want to obtain micelles as monodisperse with identical Nagg(aggregation number) in the one simulation, but distribution of sizes is broad and it is opposite of experimental results. The -reprod option only turns off various optimizations to help diagnose potential bugs. It is not relevant here. MD is chaotic; even the exact same .tpr file on the same hardware will not necessarily produce binary identical results. Hence the sampling issue. Can you help me about this problem, Please? I have no expertise in micelle simulations. In general, either longer simulations or several more simulations of intermediate length will give you better sampling from which you can gather more statistically reliable estimates of experimental observables. Note that the quality of the topology will also dictate whether or not the results will reflect reality, so proper force field derivation and validation is necessary before any results are trustworthy. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] results of md
Dear Justin, Thank you very much from your response. It means that this problem is not important. Should I use -reprod option in running of md.mdp? I want to obtain micelles as monodisperse with identical Nagg(aggregation number) in the one simulation, but distribution of sizes is broad and it is opposite of experimental results. Can you help me about this problem, Please? Best Regards Sara - Original Message - From: Justin Lemkul To: mohammad agha ; Discussion list for GROMACS users Cc: Sent: Wednesday, December 5, 2012 12:31 AM Subject: Re: [gmx-users] results of md On 12/4/12 3:57 PM, mohammad agha wrote: > Dear Gromacs Specialists, > > I ran one system (to create of micelles) tow times. Time of creation of > micelles was different in each run and for example if it has been created 5 > micelles (in the end of simulation) in both of them but the number of > molecules presence in micelles (aggregation number) is different. > > My question is that why the results of systems aren't identical? > May I ask you to answer my question, Please? > Simulations rarely are identical and hence why extensive sampling is important. Think about micelle formation under experimental conditions. How long does it take? Seconds? Minutes? I am willing to bet your simulations are orders of magnitude shorter, by necessity. Simulation time and number of simulations (replicates) are important in deriving proper statistics, but there is certainly no guarantee that two simulations will ever be exactly the same. Reproducibility is discussed very nicely on the Gromacs website. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] results of md
On 12/4/12 3:57 PM, mohammad agha wrote: Dear Gromacs Specialists, I ran one system (to create of micelles) tow times. Time of creation of micelles was different in each run and for example if it has been created 5 micelles (in the end of simulation) in both of them but the number of molecules presence in micelles (aggregation number) is different. My question is that why the results of systems aren't identical? May I ask you to answer my question, Please? Simulations rarely are identical and hence why extensive sampling is important. Think about micelle formation under experimental conditions. How long does it take? Seconds? Minutes? I am willing to bet your simulations are orders of magnitude shorter, by necessity. Simulation time and number of simulations (replicates) are important in deriving proper statistics, but there is certainly no guarantee that two simulations will ever be exactly the same. Reproducibility is discussed very nicely on the Gromacs website. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] results of md
Dear Gromacs Specialists, I ran one system (to create of micelles) tow times. Time of creation of micelles was different in each run and for example if it has been created 5 micelles (in the end of simulation) in both of them but the number of molecules presence in micelles (aggregation number) is different. My question is that why the results of systems aren't identical? May I ask you to answer my question, Please? Best Regards Sara -- 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
