Re: [gmx-users] Re: Justin umbrella sampling tutorial......
Thank you Thomas and Justin for your valuable suggestion. Thomas and Justin, my Query is as follow.. In step six ..We are doing NPT equilibration followed by production run The mdp files for both is same(Except the time of run and saving of output) So why the two mdp are same? Why we not restrain total protein for NPT equilibration (-DPOSRES) and then only POSRES_B (Position restrain on B chain, remove position restrain from other chain) for production run..(these we follow generally)??? The main reason of confusion to me is the same mdp file in Equilibration(npt_umbrella.mdp ) and production run (md_umbrella.mdp). So what is the difference between the NPT equilibration and production run.??? As per Thomas explanation I interpret the following Answer to my Queries.. Please tell me these are right or wrong *So if you want to calculate some equilibrium property of a protein in water you do first a preperation simulation to equilibrate the system (NVE, NVT or NPT - depending for what ensemble you want the property).Normally during this you put position restraints to the protein backbone, so that the protein structure does not gets disturbed during the part where you equilibrate the water. but if your protein is fairly stable / rigid, you don't need these restraints.* So as the protein is stable thats why we are not using the position restrained in NPT.. That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same. Please accept my apology if I interpret any wrong and if unable to explain you my query.. Thanks to Justin and Thomas for there valuable guidance I will be a very greatfull to you if you help me to solve my simple query.. Thank you in advance... With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
Thank you Thomas and Justin for your valuable suggestion. Thomas and Justin, my Query is as follow.. In step six ..We are doing NPT equilibration followed by production run The mdp files for both is same(Except the time of run and saving of output) So why the two mdp are same? Why we not restrain total protein for NPT equilibration (-DPOSRES) and then only POSRES_B (Position restrain on B chain, remove position restrain from other chain) for production run..(these we follow generally)??? The main reason of confusion to me is the same mdp file in Equilibration(npt_umbrella.mdp ) and production run (md_umbrella.mdp). So what is the difference between the NPT equilibration and production run.??? As per Thomas explanation I interpret the following Answer to my Queries.. Please tell me these are right or wrong * So if you want to calculate some equilibrium property of a protein in water you do first a preperation simulation to equilibrate the system (NVE, NVT or NPT - depending for what ensemble you want the property).Normally during this you put position restraints to the protein backbone, so that the protein structure does not gets disturbed during the part where you equilibrate the water. but if your protein is fairly stable / rigid, you don't need these restraints.(Thomas Explanation) * my Interpretation is as follow So as the protein is stable thats why we are not using the position restrained in NPT.. That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same. Please accept my apology if I interpret any wrong and if unable to explain you my query.. Thanks to Justin and Thomas for there valuable guidance I will be a very greatfull to you if you help me to solve my simple query.. Thank you in advance... With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
On 5/28/12 3:12 PM, rama david wrote: Thank you Thomas and Justin for your valuable suggestion. Thomas and Justin, my Query is as follow.. In step six ..We are doing NPT equilibration followed by production run The mdp files for both is same(Except the time of run and saving of output) So why the two mdp are same? Why we not restrain total protein for NPT equilibration (-DPOSRES) and then only POSRES_B (Position restrain on B chain, remove position restrain from other chain) for production run..(these we follow generally)??? The main reason of confusion to me is the same mdp file in Equilibration(npt_umbrella.mdp ) and production run (md_umbrella.mdp). So what is the difference between the NPT equilibration and production run.??? If one were to run an umbrella sampling simulation in each window without prior equilibration, you would normally discard the first few ns as equilibration. All the tutorial is telling you to do is to run some equilibration as a separate step. You can approach the equilibration however you like. As per Thomas explanation I interpret the following Answer to my Queries.. Please tell me these are right or wrong */So if you want to calculate some equilibrium property of a protein in water you do first a preperation simulation to equilibrate the system (NVE, NVT or NPT - depending for what ensemble you want the property).Normally during this you put position restraints to the protein backbone, so that the protein structure does not gets disturbed during the part where you equilibrate the water. but if your protein is fairly stable / rigid, you don't need these restraints./* So as the protein is stable thats why we are not using the position restrained in NPT.. That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same. More or less. The special case with what you're doing in the tutorial is that you have no initiating velocities in each window; you only have coordinates. That's why it makes sense to do a bit of equilibration in each window first, generating velocities and re-equilibrating the system. -Justin Please accept my apology if I interpret any wrong and if unable to explain you my query.. Thanks to Justin and Thomas for there valuable guidance I will be a very greatfull to you if you help me to solve my simple query.. Thank you in advance... With Best Wishes, Rama David. -- 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] Re: Justin umbrella sampling tutorial......
Thank you Justin for reply... More or less. The special case with what you're doing in the tutorial is that you have no initiating velocities in each window; you only have coordinates. That's why it makes sense to do a bit of equilibration in each window first, generating velocities and re-equilibrating the system. -Justin In npt_umbrella.mdp we have gen_vel = yes The command line in tutorial is grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr ... grompp -f npt_umbrella.mdp -c conf450.gro -p topol.top -n index.ndx -o npt22.tpr So if I modify the process as follow, Then is the need of equilibration (Can we skip equilibration and run production md) use -t flag with cpt ( to give velocity of the previous run ) file continuation = yes gen_vel = no . Is these alternative process is right or totally wrong..??? Please give me a valuable suggestion. Thank you in advance. With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
On 5/28/12 3:49 PM, rama david wrote: Thank you Justin for reply... More or less. The special case with what you're doing in the tutorial is that you have no initiating velocities in each window; you only have coordinates. That's why it makes sense to do a bit of equilibration in each window first, generating velocities and re-equilibrating the system. -Justin In npt_umbrella.mdp we have gen_vel = yes The command line in tutorial is grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr ... grompp -f npt_umbrella.mdp -c conf450.gro -p topol.top -n index.ndx -o npt22.tpr So if I modify the process as follow, Then is the need of equilibration (Can we skip equilibration and run production md) use -t flag with cpt ( to give velocity of the previous run ) file continuation = yes gen_vel = no . Is these alternative process is right or totally wrong..??? Using the checkpoint in this instance is wrong. The only checkpoint you have accessible to you at that point is from the end of the pulling simulation and corresponds to the final state of the system. Applying these velocities to the intermediate configurations along the reaction coordinate is likely to do weird and unreliable things to the trajectory. It is more robust to run NPT and then data collection, or as I said before, proceed immediately to a continuous data collection (with gen_vel = yes!) and discard the initial few ns of data as equilibration. In theory, this procedure is no different than any other simulation that one conducts. -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] Re: Justin umbrella sampling tutorial......
Thank you Justin.. Is these alternative process is right or totally wrong..??? Using the checkpoint in this instance is wrong. The only checkpoint you have accessible to you at that point is from the end of the pulling simulation and corresponds to the final state of the system. Applying these velocities to the intermediate configurations along the reaction coordinate is likely to do weird and unreliable things to the trajectory. It is more robust to run NPT and then data collection, or as I said before, proceed immediately to a continuous data collection (with gen_vel = yes!) and discard the initial few ns of data as equilibration. In theory, this procedure is no different than any other simulation that one conducts. Check point file has velocity of the last co-ordinates and we are using middle configuration.. Thank you for explaination ... I have another query.. In npt equilibration can I use define = -DPOSRES (Position restrain all the protein along the chain B) and in production md define = -DPOSRES_B ( Position restrain for chain B only..) ??? If not What is appropriate reason??? Thank you in advance... With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Justin umbrella sampling tutorial......
On 5/28/12 4:09 PM, rama david wrote: Thank you Justin.. Is these alternative process is right or totally wrong..??? Using the checkpoint in this instance is wrong. The only checkpoint you have accessible to you at that point is from the end of the pulling simulation and corresponds to the final state of the system. Applying these velocities to the intermediate configurations along the reaction coordinate is likely to do weird and unreliable things to the trajectory. It is more robust to run NPT and then data collection, or as I said before, proceed immediately to a continuous data collection (with gen_vel = yes!) and discard the initial few ns of data as equilibration. In theory, this procedure is no different than any other simulation that one conducts. Check point file has velocity of the last co-ordinates and we are using middle configuration.. Thank you for explaination ... I have another query.. In npt equilibration can I use define = -DPOSRES (Position restrain all the protein along the chain B) and in production md define = -DPOSRES_B ( Position restrain for chain B only..) ??? If not What is appropriate reason??? You can use either. I have never tried it, but there is no reason to believe there will be any substantive reason during data collection. The production MD period is significantly longer than the equilibration, and the results will likely turn out the same, when considering error estimates. Sufficient sampling of any series of simulations should converge. -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] Re: Justin umbrella sampling tutorial......
Thank you Justin for giving your valuable time to solve my stupid problems. You can use either. I have never tried it, but there is no reason to believe there will be any substantive reason during data collection. The production MD period is significantly longer than the equilibration, and the results will likely turn out the same, when considering error estimates. Sufficient sampling of any series of simulations should converge. -Justin With Best Wishes, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Justin umbrella sampling tutorial......
I think all the answers to your question are in the tutorial. Probably read first the lysozyme tutorial and then the umbrella tutorial again. But here is a more general answer: Normally you have two types of simulations: preperation (which is also equilibration) production and the need of restraints depends on what you want to achive. So if you want to calculate some equilibrium property of a protein in water you do first a preperation simulation to equilibrate the system (NVE, NVT or NPT - depending for what ensemble you want the property). Normally during this you put position restraints to the protein backbone, so that the protein structure does not gets disturbed during the part where you equilibrate the water. but if your protein is fairly stable / rigid, you don't need these restraints. Then you do the production simulation. Normally without restraints, since you want to know the property for a protein in equilibrium. But you could also do this with the same position restraints, in the extrem case, when you freeze the protein, you would get the property for a special protein geometry (the one to which ou restrain the coordinates). - So it really depends on what you want to do!!! For the umbrella tutorial: As far as i remember, Justin used the restrains for one of the chains (B), so to conserve the structure of said chain, because when one pull chain A away this would have an influence to the structure of chain B (they interact with each other). BUT: one could also dismiss these restrains during the umbrella simulations, since it is expected the structure of chain B depends on the distance to chain A (since they interact). You could also restrain only that part of chain B, which does not interact directly with chain A, to conserve a part of the structure of B (so you would be in the middle between the two extreme cases above). In all three cases you get a different answer (like above for the equilibrium property). One could argue which is the better option, but i think all three have their right to exist, since the answer to this also depends on the initial question. Best would be to do all three cases, but mostly one does not have so much time. So one must stick to one. Which leads to: First think about your question. Then think about how to answer it (think often there will be different possibilities / methods). Then decide what to do... Since the answer you get (may) depend on the method you use, you should justify your decission. Hope this helps greetings thomas Thank you Justin for these correct explanation Its really clear my lot of queries.. For the tutorial, NPT is conducted with restraints on all protein heavy atoms. The production runs are conducted by restraining only one chain for practical reasons. These is my question ; If we are doing NPT with restraints on all protein atom and production run by conducted by restraining only one chain for protein... means NPT and productin run mdp files should be different , Where these information in mdp files??? It my request to you please tell me why these mdp files are almost same in parameter .. (Where you mentioned in mdp for npt to do restraints on all proteins heavy atoms and for production md restraining only one chain ..) I don't understand what more I can say beyond what I already have. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Justin umbrella sampling tutorial...... (rama david)
For your second problem: you have to create this file by writing the group numbers, which inform the script to decide which two groups to be selected for distance calculation. If you made it, you first problem would probably be solved. Good luck, Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands Message: 4 Date: Wed, 23 May 2012 19:18:56 +0530 From: rama david ramadavidgr...@gmail.com Subject: [gmx-users] Justin umbrella sampling tutorial.. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAD=-syhie5kxqj9fgdhqykqav0vusyc-atshblgs5cqirfu...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi Gromacs Friends, I am performing justin tutorial for umbrella sampling .. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html I encounter with following problem while using the disatances.pl script 1. After command perl distances.pl I got following message ... Use of uninitialized value $distance in concatenation (.) or string at distances.pl line 30. readline() on closed filehandle IN at distances.pl line 16. What may be reason for these .. 2. What is the groups.txt ?? Where it will find ?? Why it is needed?? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120523/3cbd7a8f/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 97, Issue 179 ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: Justin umbrella sampling tutorial...... (rama david)
On Wed, May 23, 2012 at 7:30 PM, Du Jiangfeng (BIOCH) j...@maastrichtuniversity.nl wrote: For your second problem: you have to create this file by writing the group numbers, which inform the script to decide which two groups Thank you... Du Jiangfeng Yes problem get solve!!! Thank you With Best Wishes, Rama David -- 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
