Re: [gmx-users] Justin umbrella sampling tutorial......
Thank you for your reply, I am asking you again same question, EXTREMELY SORRY for my stupidity, In step six , I unable to differentiate npt and production run by mdp file as usualy we find difference by define term, I think I get meaning upto reason why to use -DPOSRES_B, but I want to know if we are using same mdp file in both condition means the npt equilibriation is as same as md production , Then why to do npt, just run production md with DPOSRES_B With my 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] Justin umbrella sampling tutorial......
On 5/24/12 8:19 AM, rama david wrote: Thank you for your reply, I am asking you again same question, EXTREMELY SORRY for my stupidity, In step six , I unable to differentiate npt and production run by mdp file as usualy we find difference by define term, I think I get meaning upto reason why to use -DPOSRES_B, but I want to know if we are using same mdp file in both condition means the npt equilibriation is as same as md production , Then why to do npt, just run production md with DPOSRES_B I'm not sure of what the question is exactly, so my apologies if the following explanation does not answer it. 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. Don't confuse yourself by always assuming that the difference between NPT and production runs is the use of define statements or position restraints. There are many ways of doing equilibration. NPT of a protein in solvent is typically done with restraints on the protein, allowing the solvent to relax and avoiding potential geometric distortions due to bad solvent contacts. Production runs may or may not make use of any restraints. Their use is dependent upon the situation at hand and whether or not they are appropriate. I hope this explanation makes everything clear. -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] Justin umbrella sampling tutorial......
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 ..) Please accept my apology if I unable to explain you my problem 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] Justin umbrella sampling tutorial......
On 5/24/12 6:35 AM, rama david wrote: 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 -- 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] Justin umbrella sampling tutorial......
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?? -- 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] Justin umbrella sampling tutorial......
On 5/23/12 3:48 PM, rama david wrote: 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 http://disatances.pl script 1. After command perl distances.pl http://distances.pl I got following message ... Use of uninitialized value $distance in concatenation (.) or string at distances.pl http://distances.pl line 30. readline() on closed filehandle IN at distances.pl http://distances.pl line 16. What may be reason for these .. The required input doesn't exist. Either you omitted a step or you're executing the script in the wrong directory. 2. What is the groups.txt ?? Where it will find ?? Why it is needed?? This is stated in the tutorial. -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] Justin umbrella sampling tutorial......
Thank you justin.. I solve script problem.. I have another query .. As mention in tutorial , In step six , we have to do brief NPT equilibration npt_umbrella.mdp link is http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp After these we have to run MD ...mdp file link is http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_umbrella.mdp 1. In both case define is same.. In general When we are doing NPT we are position restrain whole protein backbone , But in these case we are only restrain chain B...Please explain in detail ... 2. The difference in mdp file is at gen_vel, and run time 100 ps for npt , 10 ns for md If both mdp file is same Then why to do separate npt and md ( Is the only reason is to generate velocity in npt simulation ??? Why we are not using velocity from pull *(step five)* ) 3 . If we are using the gen_vel = yes continuation= yes If continuation is yes, then why gen_vel is yes Please shade some light on meaning of continuation and gen_vel 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] Justin umbrella sampling tutorial......
On 5/24/12 7:11 AM, rama david wrote: Thank you justin.. I solve script problem.. I have another query .. As mention in tutorial , In step six , we have to do brief NPT equilibration npt_umbrella.mdp link is http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp After these we have to run MD ...mdp file link is http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_umbrella.mdp 1. In both case define is same.. In general When we are doing NPT we are position restrain whole protein backbone , But in these case we are only restrain chain B...Please explain in detail ... Please read the paper we published using this system. It explains the conceptual details. 2. The difference in mdp file is at gen_vel, and run time 100 ps for npt , 10 ns for md If both mdp file is same Then why to do separate npt and md ( Is the only reason is to generate velocity in npt simulation ??? Why we are not using velocity from pull /(step five)/ ) 3 . If we are using the gen_vel = yes continuation= yes If continuation is yes, then why gen_vel is yes Please shade some light on meaning of continuation and gen_vel At this point, you're basically starting a new simulation in the absence of a net pull force. You're using the umbrella potential as a restraint, not to bias the motion, so you're re-equilibrating. The use of continuation = yes simply implies that the starting configuration has already been constrained and thus the constraints should not be reset. In this context, the difference between yes and no is likely not particularly relevant. -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] Justin umbrella sampling tutorial......
Hi Justin, Thank you for your Reply Before start tutorial I read your paper, It help me a lot to understand the concept of umbrella sampling... But truly I not understand the part in six step why to use define -DPOSRES_B and not -DPOSRES, I think I miss it ... I will be a very greatfull to you, if you shade some light on these Sorry for trouble Thank you in advance With best wishes, Rama David 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] Justin umbrella sampling tutorial......
On 5/24/12 7:40 AM, rama david wrote: Hi Justin, Thank you for your Reply Before start tutorial I read your paper, It help me a lot to understand the concept of umbrella sampling... But truly I not understand the part in six step why to use define -DPOSRES_B and not -DPOSRES, I think I miss it ... I will be a very greatfull to you, if you shade some light on these Using -DPOSRES_B restrains only one chain of the protein, thus mimicking the stability of a larger macromolecular assembly. Using -DPOSRES restrains all protein chains, which accomplishes nothing when trying to do umbrella sampling. The chain to which the umbrella potential is applied would not be able to move at all, thus rendering the pull force measurements ineffectual. -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
