Re: [gmx-users] About MD
On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all， A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. 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] About MD
Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? I wonder to know how can I set the parameters and in which condition I obtain the structure by thermodynamics, and in which condition (with which parameter setting) I can obtain the structure by kinetics. MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Do you mean that I can obtain the structure by thermodynamics in longer and higher temperature ; obtain the structure by kinetics in shorter and lower temperature? 2011/9/26 Mark Abraham mark.abra...@anu.edu.au On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all， A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About MD
On 26/09/2011 5:31 PM, xiaojing gong wrote: Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? I wonder to know how can I set the parameters and in which condition I obtain the structure by thermodynamics, and in which condition (with which parameter setting) I can obtain the structure by kinetics. MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Do you mean that I can obtain the structure by thermodynamics in longer and higher temperature ; obtain the structure by kinetics in shorter and lower temperature? You are drawing some artificial distinction whose purpose I do not understand. A short simulation on a FES at a temperature low enough that the barriers are larger than the readily available KE will be kinetically trapped. I'd guess that most MD simulations that have ever been run have suffered from this defect. The shape of the FES will generally vary with temperature also. Mark 2011/9/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all, A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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] About MD
Hi, many thanks. I am doing some simulation correlated with the growth, in experiments, there are two kinds of growth, one is driven by kinetics and other is by thermodynamics. So I just wonder to know by using MD simulations, the results I obtained is driven by kinetics or thermodynamics. Silly question. XJ 2011/9/26 Mark Abraham mark.abra...@anu.edu.au On 26/09/2011 5:31 PM, xiaojing gong wrote: Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? I wonder to know how can I set the parameters and in which condition I obtain the structure by thermodynamics, and in which condition (with which parameter setting) I can obtain the structure by kinetics. MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Do you mean that I can obtain the structure by thermodynamics in longer and higher temperature ; obtain the structure by kinetics in shorter and lower temperature? You are drawing some artificial distinction whose purpose I do not understand. A short simulation on a FES at a temperature low enough that the barriers are larger than the readily available KE will be kinetically trapped. I'd guess that most MD simulations that have ever been run have suffered from this defect. The shape of the FES will generally vary with temperature also. Mark 2011/9/26 Mark Abraham mark.abra...@anu.edu.au On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all， A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. 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 -- 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
Re: [gmx-users] About MD
On 26/09/2011 6:25 PM, xiaojing gong wrote: Hi, many thanks. I am doing some simulation correlated with the growth, in experiments, there are two kinds of growth, one is driven by kinetics and other is by thermodynamics. To address this question, I think you need to seek a better description than driven by thermodynamics. All processes are driven by thermodynamics. So I just wonder to know by using MD simulations, the results I obtained is driven by kinetics or thermodynamics. The two growth modes must differ somehow in the conditions that trigger them. For a valid model, which mode you might see will depend what conditions you choose. Mark Silly question. XJ 2011/9/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 26/09/2011 5:31 PM, xiaojing gong wrote: Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? I wonder to know how can I set the parameters and in which condition I obtain the structure by thermodynamics, and in which condition (with which parameter setting) I can obtain the structure by kinetics. MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Do you mean that I can obtain the structure by thermodynamics in longer and higher temperature ; obtain the structure by kinetics in shorter and lower temperature? You are drawing some artificial distinction whose purpose I do not understand. A short simulation on a FES at a temperature low enough that the barriers are larger than the readily available KE will be kinetically trapped. I'd guess that most MD simulations that have ever been run have suffered from this defect. The shape of the FES will generally vary with temperature also. Mark 2011/9/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all, A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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] About MD
On Mon, 26 Sep 2011 09:31:39 +0200 xiaojing gong xnz...@gmail.com wrote: Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? The energy is NOT minimized in thermodynamics. The relevant quantity that is minimized is the free energy. In NVT-simulations it's the Helmholtz free energy F = E - TS where T is temperature and S the entropy. The minimum of F is obtained in the struggle of minimum energy and maximal entropy. E is, however, minimized when T=0. In NpT you minimize the Gibbs free energy G = E + pV -TS where p is pressure and V is volume. Here to minimize E you would set p=0=T. -- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland Jussi Lehtola, FM Tohtorikoulutettava jussi.leht...@helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about md simulation
amri ta wrote: Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? These should help. http://wiki.gromacs.org/index.php/Errors#LINCS_warnings http://wiki.gromacs.org/index.php/blowing_up http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about md simulation
Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? The md.log file reads: Initializing LINear Constraint Solver number of constraints is 2365 average number of constraints coupled to one constraint is 2.5 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.336565 691 696 0.033770 After LINCS 0.342830698700 0.028042 Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.858278 (between atoms 3397 and 3398) rms 0.016634 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3395 3398 76.20.1341 0.0446 0.1470 3398 3399 78.80.1341 0.0492 0.1470 Constraint error in algorithm Lincs at step -1 Grid: 10 x 10 x 10 cells Configuring nonbonded kernels Testing x86_64 SSE supports...presents Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 70.089874 1537 1456 0.559021 After LINCS 29.983810 3223 32240.787549 Like this, errors showed Constraint error in algorithm Lincs at step 0, step1 and the simulation stops at step 1. Do I have to modify my md.mdp to remedy this? Your advice is appreciated. Best regards, Amrita Ghosh National Institute of Mental Health and Neurosciences, Bangalore-29. India. 5, 50, 500, 5000 - Store N number of mails in your inbox. Go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about md simulation
Hi Amrita, I have faced similar problem.before MD run, try to minimize water box and protein seperately with both CG and SD, then put protein in the water box and minimize it again .., then go for MD run, I think after that you dont have any Lincs warning.. Chiradip --- amri ta [EMAIL PROTECTED] wrote: Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? The md.log file reads: Initializing LINear Constraint Solver number of constraints is 2365 average number of constraints coupled to one constraint is 2.5 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.336565 691 696 0.033770 After LINCS 0.342830698 700 0.028042 Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.858278 (between atoms 3397 and 3398) rms 0.016634 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3395 3398 76.20.1341 0.0446 0.1470 3398 3399 78.80.1341 0.0492 0.1470 Constraint error in algorithm Lincs at step -1 Grid: 10 x 10 x 10 cells Configuring nonbonded kernels Testing x86_64 SSE supports...presents Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 70.089874 1537 1456 0.559021 After LINCS 29.983810 3223 3224 0.787549 Like this, errors showed Constraint error in algorithm Lincs at step 0, step1 and the simulation stops at step 1. Do I have to modify my md.mdp to remedy this? Your advice is appreciated. Best regards, Amrita Ghosh National Institute of Mental Health and Neurosciences, Bangalore-29. India. 5, 50, 500, 5000 - Store N number of mails in your inbox. Go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Chiradip Chatterjee Senior research fellow Structural Biology Division Department of Biological Science National University of Singapore Phone:65-92301295 E-mail:[EMAIL PROTECTED] [EMAIL PROTECTED] Home Page: www.chem.ucsb.edu/~cchatterjee/ I LOVE KOLKATA ___ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about md simulation
Also see http://wiki.gromacs.org/index.php/Thermostats As you do not want to temperature couple the sodium ions independently Tom --On Tuesday, September 11, 2007 18:14:43 +1000 Mark Abraham [EMAIL PROTECTED] wrote: amri ta wrote: Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? These should help. http://wiki.gromacs.org/index.php/Errors#LINCS_warnings http://wiki.gromacs.org/index.php/blowing_up http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
