[gmx-users] AFM pulling simulations
Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, -- 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] AFM pulling simulations
X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] AFM pulling simulations
http://www.gromacs.org/Documentation/Tutorials On 03/22/2011 11:02 AM, X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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] AFM pulling simulations
Thanks Justin, That is pretty much the only tutorial one can found. I have one question now, how do I force a particular orientation of my protein during genbox (for example if i need to pull along N-C vector, i need my protein oriented that way, i.e in Z direction for example to later apply the force in that direction). Date: Tue, 22 Mar 2011 11:15:54 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] AFM pulling simulations X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] AFM pulling simulations
too eager to send an email.. I think playing with editconf with princ flag should do the trick .. sorry folks and thanks for the help !! From: xru...@live.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM pulling simulations Date: Tue, 22 Mar 2011 15:47:41 + Thanks Justin, That is pretty much the only tutorial one can found. I have one question now, how do I force a particular orientation of my protein during genbox (for example if i need to pull along N-C vector, i need my protein oriented that way, i.e in Z direction for example to later apply the force in that direction). Date: Tue, 22 Mar 2011 11:15:54 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] AFM pulling simulations X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 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] AFM Pulling Simulations
On 26/08/10 19:56, chris.ne...@utoronto.ca wrote: Natalie: It would also be a good idea for you to ensure that your supervisor knows how difficult it is to learn and correctly apply these methods. If they think that a person can learn linux and gromacs and the gromacs pull code in a short period of time, then the stage is set for frustration and ultimate disaster. Lots of people think that these things are plug and play -- of course, they are not. If you don't have a mentor nearby who can help you, then figuring this all out and getting some meaningful data could easily take you a year. I don't mean to scare you off, but it is true that while no professor asks a new student to get protein crystals within a few months, that request is often made for simulation results from experimental supervisors. Perhaps the gromacs community should be working toward getting testimonials to the significant amount of time that it can take to learn to run simulations properly on the gromacs site that new users could direct their supervisors to in the case that those supervisors are not acquainted with molecular simulation. I couldn't agree more. I have been thrown into learning GROMACS and designing a coarse grain model from scratch (my background is that of an experimentalist, doing AFM pulling experiments, by the way!), all practically by myself. I mean: I *wanted* to learn all of that, I just didn't expect I would have done it *alone*. So I read the Frenkel-Smit book, the GROMACS manual, and banged my head a lot (luckly I was already experienced with Linux and programming). No wonder one year after, I'm just beginning to see where I am going *sigh*. m. Chris. Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx There is a steered MD component to the umbrella sampling tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling Though it is an excellent reference, the manual will not teach you everything you need to know. The mailing list archive (although currently glitching) and Google are your friends, as well. There are hundreds of threads in the archive about pull code success and failure, at least some of which should be informative :) Thanks loads!! I'll give it a try! Natalie xxx -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/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/mailing_lists/users.php
[gmx-users] AFM Pulling Simulations
Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] AFM Pulling Simulations
Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx There is a steered MD component to the umbrella sampling tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling Though it is an excellent reference, the manual will not teach you everything you need to know. The mailing list archive (although currently glitching) and Google are your friends, as well. There are hundreds of threads in the archive about pull code success and failure, at least some of which should be informative :) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php
Re: [gmx-users] AFM Pulling Simulations
Quoting Justin A. Lemkul jalem...@vt.edu: Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx There is a steered MD component to the umbrella sampling tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling Though it is an excellent reference, the manual will not teach you everything you need to know. The mailing list archive (although currently glitching) and Google are your friends, as well. There are hundreds of threads in the archive about pull code success and failure, at least some of which should be informative :) Thanks loads!! I'll give it a try! Natalie xxx -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] AFM Pulling Simulations
Natalie: It would also be a good idea for you to ensure that your supervisor knows how difficult it is to learn and correctly apply these methods. If they think that a person can learn linux and gromacs and the gromacs pull code in a short period of time, then the stage is set for frustration and ultimate disaster. Lots of people think that these things are plug and play -- of course, they are not. If you don't have a mentor nearby who can help you, then figuring this all out and getting some meaningful data could easily take you a year. I don't mean to scare you off, but it is true that while no professor asks a new student to get protein crystals within a few months, that request is often made for simulation results from experimental supervisors. Perhaps the gromacs community should be working toward getting testimonials to the significant amount of time that it can take to learn to run simulations properly on the gromacs site that new users could direct their supervisors to in the case that those supervisors are not acquainted with molecular simulation. Chris. Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx There is a steered MD component to the umbrella sampling tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling Though it is an excellent reference, the manual will not teach you everything you need to know. The mailing list archive (although currently glitching) and Google are your friends, as well. There are hundreds of threads in the archive about pull code success and failure, at least some of which should be informative :) Thanks loads!! I'll give it a try! Natalie xxx -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/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/mailing_lists/users.php
[gmx-users] AFM pulling rate
Hi, The unit of the afm_rate in the GROMACS manual 3.3-1 is nm/ps. I have read something in an earlier thread on this list that this might be a typo, it should be nm/timestep. Does anyone know? I would be happy if I could have that information. Moreover, I am a bit confused about the output in the .pdo-file. In the description of .pdo-files on page 113 in the manual 3.3.-1 it is written that the .pdo file will contain calculated forces from AFM-pulling simulation. On the other hand, on page 118, the description of the AFM output is that it only contains positions of reference group, pulled group and spring. This is also the only information I can find in my output. I wonder if there is a way to get the calculated force into the pdo file or if it should be done manually (force=k*extension)? /Malin Bergenstråhle ___ 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] AFM pulling rate
Hi, The pull code in Gromacs 3 is pretty messy. The rate is in nm/ps. The force is (unfortunately) not written to the pdo file. You have to redetermine it from the positions, but beware that one of the two groups could jump over the periodic boundary. In Gromacs 4 (and the current CVS) I have completely rewritten the pull code. There are separate xvg output files with only the positions and only the forces. Berk. Date: Thu, 14 Aug 2008 08:30:35 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] AFM pulling rate Hi, The unit of the afm_rate in the GROMACS manual 3.3-1 is nm/ps. I have read something in an earlier thread on this list that this might be a typo, it should be nm/timestep. Does anyone know? I would be happy if I could have that information. Moreover, I am a bit confused about the output in the .pdo-file. In the description of .pdo-files on page 113 in the manual 3.3.-1 it is written that the .pdo file will contain calculated forces from AFM-pulling simulation. On the other hand, on page 118, the description of the AFM output is that it only contains positions of reference group, pulled group and spring. This is also the only information I can find in my output. I wonder if there is a way to get the calculated force into the pdo file or if it should be done manually (force=k*extension)? /Malin Bergenstråhle ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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
[gmx-users] AFM pulling: after bond-breakage force does not drop to zero
Dear all, I simulate pulling experiment with the AFM-option in GROMACS. I calculate the forces from the .pdo file: F = k_c (/spr/ - /pullg/) with F the force, k_c the springconstant. spring is the position of the spring and /pullg/ the position of the pullgroup. after the bond-breakage the forces have a much lower value, but they do not drop to zero. in this picture is one of my force-distance-curves: http://www.students.uni-mainz.de/schlesie/diplomarbeit/force-distance-curve.JPG My problem is I do not understand why (after the bond-breakage) the mean value of the force is not zero. The simulations are made in vacuum, so there is no friction. When I use a lower the springconstant the distance (/spr/ - /pullg/) gets greater. Greater springconstant yields a lower distance. Has anybody of you an idea why the mean value of the forces does not drop to zero, or have seen anything similar? Thanks for an answer. Thomas ___ 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
[gmx-users] AFM pulling: after bond-breakage force does not drop to zero
Dear all, I simulate pulling experiment with the AFM-option in GROMACS. I calculate the forces from the .pdo file: F = k_c (/spr/ - /pullg/) with F the force, k_c the springconstant. spring is the position of the spring and /pullg/ the position of the pullgroup. after the bond-breakage the forces have a much lower value, but they do not drop to zero. in this picture is one of my force-distance-curves: http://www.students.uni-mainz.de/schlesie/diplomarbeit/force-distance-curve.JPG My problem is I do not understand why (after the bond-breakage) the mean value of the force is not zero. The simulations are made in vacuum, so there is no friction. When I use a lower the springconstant the distance (/spr/ - /pullg/) gets greater. Greater springconstant yields a lower distance. Has anybody of you an idea why the mean value of the forces does not drop to zero, or have seen anything similar? Thanks for an answer. Thomas ___ 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
[gmx-users] AFM Pulling index.ndx pull.ppa
Hello, I am attempting to use AFM pulling on a 17 amino acid peptide, but am having trouble with the 'group' concept. I've read the manual and searched sample XXX.ndx files, but have had no luck. How would I define the first amino acid as the reference group (i.e. - fixed in space) and the last amino acid in the peptide as group 1 (i.e. - amino acid at which the spring acts). The first amino acid is Alanine and the last is Leucine. Is a sample .ndx file available? The second issue is with the afm_init value in the pull.ppa file. If I understand correctly it is the center of mass vector of the peptide, and should go from the reference group to the pulled group ( from first amino acid A to last amino acid L). How is this vector calculated and what is the syntax used to enter this vector in the pull.ppa file. Any help is appreciated. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ 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] AFM Pulling and com motion
From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM Pulling and com motion Date: Fri, 21 Sep 2007 00:49:21 +0800 Thanks for your reply. There is no absolute reference here. The system is just from this web site http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007; (hands-on: The pull package). I really do not know the advantage or necessity of stopcm in SMD, because when I test the two systems, with and without stopcm, there is a distinct difference between the calculated pull force. MD is chaotic, so changing any detail will change the course of the simulation. Any ensemble averages should be the same, but for short runs, as the course example, you do not reach the ensemble average. I guess this is the reason for the difference. Berk. _ Live Search, for accurate results! http://www.live.nl ___ 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] AFM Pulling and com motion
From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM Pulling and com motion Date: Thu, 20 Sep 2007 11:06:09 +0800 Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is comm-mode=Linear and comm-grps=System. I was confused about it as I believed we should not stopcm when doing AFM Pulling because of the external force. Does it problematic to stopcm when doing AFM Pulling? Thanks! This depends on what type of pulling you are doing. If you have an absolute reference you are right. But when you pull between two groups of atoms, there are no external forces, but internal forces between two groups. Berk. _ FREE pop-up blocking with the new Windows Live Toolbar - get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ ___ 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] AFM Pulling and com motion
Thanks to Berk. I just tested two system, one with stopcm and the other without stopcm. I calculated the pull forces and compared them with each other. There are really some distinct differences between them during the 80ps simulation. I worry about it, for example, in long time simulations, so I want to know which one is the better and reliable choice, stopcm or without stopcm. As I know, the NAMD package only removes the initial center of mass motion. Thanks for your reply. Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is comm-mode=Linear and comm-grps=System. I was confused about it as I believed we should not stopcm when doing AFM Pulling because of the external force. Does it problematic to stopcm when doing AFM Pulling? Thanks! This depends on what type of pulling you are doing. If you have an absolute reference you are right. But when you pull between two groups of atoms, there are no external forces, but internal forces between two groups. Berk. ___ 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] AFM Pulling and com motion
You didn't tell if you are using an absolute reference or not. With an absolute reference you should not remove the com motion. Berk. From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM Pulling and com motion Date: Thu, 20 Sep 2007 22:44:29 +0800 Thanks to Berk. I just tested two system, one with stopcm and the other without stopcm. I calculated the pull forces and compared them with each other. There are really some distinct differences between them during the 80ps simulation. I worry about it, for example, in long time simulations, so I want to know which one is the better and reliable choice, stopcm or without stopcm. As I know, the NAMD package only removes the initial center of mass motion. Thanks for your reply. Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is comm-mode=Linear and comm-grps=System. I was confused about it as I believed we should not stopcm when doing AFM Pulling because of the external force. Does it problematic to stopcm when doing AFM Pulling? Thanks! This depends on what type of pulling you are doing. If you have an absolute reference you are right. But when you pull between two groups of atoms, there are no external forces, but internal forces between two groups. Berk. ___ 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 _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ 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] AFM Pulling and com motion
Thanks for your reply. There is no absolute reference here. The system is just from this web site http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007; (hands-on: The pull package). I really do not know the advantage or necessity of stopcm in SMD, because when I test the two systems, with and without stopcm, there is a distinct difference between the calculated pull force. You didn't tell if you are using an absolute reference or not. With an absolute reference you should not remove the com motion. Berk. From: Zhou Bo [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM Pulling and com motion Date: Thu, 20 Sep 2007 22:44:29 +0800 Thanks to Berk. I just tested two system, one with stopcm and the other without stopcm. I calculated the pull forces and compared them with each other. There are really some distinct differences between them during the 80ps simulation. I worry about it, for example, in long time simulations, so I want to know which one is the better and reliable choice, stopcm or without stopcm. As I know, the NAMD package only removes the initial center of mass motion. Thanks for your reply. Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is comm-mode=Linear and comm-grps=System. I was confused about it as I believed we should not stopcm when doing AFM Pulling because of the external force. Does it problematic to stopcm when doing AFM Pulling? Thanks! This depends on what type of pulling you are doing. If you have an absolute reference you are right. But when you pull between two groups of atoms, there are no external forces, but internal forces between two groups. Berk. ___ 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 _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 41, Issue 73 * ___ 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
[gmx-users] AFM Pulling and com motion
Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is comm-mode=Linear and comm-grps=System. I was confused about it as I believed we should not stopcm when doing AFM Pulling because of the external force. Does it problematic to stopcm when doing AFM Pulling? Thanks! ___ 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
[gmx-users] AFM Pulling
Hi GXM Users, I'm trying to execute some AFM pulling. My index file contains two groups, [TopPeptide] and [DMPC]. I execute grompp, then when I try to execute mdrun: [EMAIL PROTECTED] SteeredMD]$ mdrun -s SMD-01.tpr -o SMD-01 -c AfterSMD-01 -e SMD-01 -g SMD-01 -pi PeptidePull.ppa -pn System.ndx -po PeptidePull -pdo PeptidePull I get a prompt, asking me to select groups: Back Off! I just backed up SMD-01.edr to ./#SMD-01.edr.3# Group 0 ( TopPeptide) has 72 elements Group 1 ( DMPC) has 5888 elements Select a group: 0 My question is: If I've already specified the group and the reference group (in the PeptidePull.ppa file, which I've pasted below for your reference) and if these groups are defined in the System.ndx file, then why am I being prompted to select a group??? (incidently, when I do select a group, I get several warnings that state "Unkown left-hand afm_rate (or afm_k1, or afm_direction, etc etc) in parameter file". Seems like it's not reading my PeptidePull.ppa file correctly). Would greatly appreciate any assistance, Arneh ; GENERAL verbose = no Skip steps = 1 ; Runtype: afm, constraint, umbrella runtype = afm ; Number of pull groups ngroups = 1 ; Groups to be pulled group_1 = TopPeptide ; The group for the reaction force. reference_group = DMPC ; Weights for all atoms in each group (default all 1) weights_1 = reference_weights = ; Ref. type: com, com_t0, dynamic, dynamic_t0 reftype = com_t0 ; Use running average for reflag steps for com calculation reflag = 10 ; Select components for the pull vector. default: Y Y Y pulldim = N N Y ; DYNAMIC REFERENCE GROUP OPTIONS ; Cylinder radius for dynamic reaction force groups (nm) r = 0 ; Switch from r to rc in case of dynamic reaction force rc = 0 ; Update frequency for dynamic reference groups (steps) update = 1 ; CONSTRAINT RUN OPTIONS ; Direction, default: 0 0 0, no direction constraint_direction = 0.0 0.0 0.0 ; Constraint distance (nm), default: 0, use starting distance constraint_distance1 = 0 ; Rate of chance of the constraint length, in nm/ps constraint_rate1 = 0 ; Tolerance of constraints, in nm constraint_tolerance = 1e-06 ; AFM OPTIONS ; Pull rates in nm/ps afm_rate1 = 0.0064 ; Force constants in kJ/(mol*nm^2) afm_k1 = 500 ; Directions afm_dir1 = 0 0 -1 ; Initial spring positions afm_init1 = 0.40434290838 0.41850681958 3.19817446605 ; UMBRELLA SAMPLING OPTIONS ; Force constants for umbrella sampling in kJ/(mol*nm^2) ; Centers of umbrella potentials with respect to reference: ; Ref - Pull. K1 = 0 Pos1 = 0.0 0.0 0.0 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] AFM Pulling
Hi all, nevermind, I caught my own mistake. (I hope this might be useful for someone in the future). PeptidePull.ppa is my input file, specifying the parameters for my pulling. -po PeptidePull is the output file. The problem here is that I used the same name. When it crossed over to another node, the wrong ppa file was read. So the moral of the story is: When running AFM pulling in parallel, make sure that the names following -pi and -po differ! (something like, -pi PeptidePull -po ExtraPeptidePull). Thanks! Arneh Arneh Babakhani wrote: Hi GXM Users, I'm trying to execute some AFM pulling. My index file contains two groups, [TopPeptide] and [DMPC]. I execute grompp, then when I try to execute mdrun: [EMAIL PROTECTED] SteeredMD]$ mdrun -s SMD-01.tpr -o SMD-01 -c AfterSMD-01 -e SMD-01 -g SMD-01 -pi PeptidePull.ppa -pn System.ndx -po PeptidePull -pdo PeptidePull * I get a prompt, asking me to select groups: *Back Off! I just backed up SMD-01.edr to ./#SMD-01.edr.3# Group 0 ( TopPeptide) has72 elements Group 1 (DMPC) has 5888 elements Select a group: 0 * My question is: If I've already specified the group and the reference group (in the PeptidePull.ppa file, which I've pasted below for your reference) and if these groups are defined in the System.ndx file, then why am I being prompted to select a group??? (incidently, when I do select a group, I get several warnings that state Unkown left-hand afm_rate (or afm_k1, or afm_direction, etc etc) in parameter file. Seems like it's not reading my PeptidePull.ppa file correctly). Would greatly appreciate any assistance, Arneh ; GENERAL verbose = no Skip steps = 1 ; Runtype: afm, constraint, umbrella runtype = afm ; Number of pull groups ngroups = 1 ; Groups to be pulled group_1 = TopPeptide ; The group for the reaction force. reference_group = DMPC ; Weights for all atoms in each group (default all 1) weights_1= reference_weights= ; Ref. type: com, com_t0, dynamic, dynamic_t0 reftype = com_t0 ; Use running average for reflag steps for com calculation reflag = 10 ; Select components for the pull vector. default: Y Y Y pulldim = N N Y ; DYNAMIC REFERENCE GROUP OPTIONS ; Cylinder radius for dynamic reaction force groups (nm) r= 0 ; Switch from r to rc in case of dynamic reaction force rc = 0 ; Update frequency for dynamic reference groups (steps) update = 1 ; CONSTRAINT RUN OPTIONS ; Direction, default: 0 0 0, no direction constraint_direction = 0.0 0.0 0.0 ; Constraint distance (nm), default: 0, use starting distance constraint_distance1 = 0 ; Rate of chance of the constraint length, in nm/ps constraint_rate1 = 0 ; Tolerance of constraints, in nm constraint_tolerance = 1e-06 ; AFM OPTIONS ; Pull rates in nm/ps afm_rate1= 0.0064 ; Force constants in kJ/(mol*nm^2) afm_k1 = 500 ; Directionsafm_dir1 = 0 0 -1 ; Initial spring positions afm_init1= 0.40434290838 0.41850681958 3.19817446605 ; UMBRELLA SAMPLING OPTIONS ; Force constants for umbrella sampling in kJ/(mol*nm^2) ; Centers of umbrella potentials with respect to reference: ; Ref - Pull. K1 = 0 Pos1 = 0.0 0.0 0.0 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] AFM pulling
From: Susanna Hug [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM pulling Date: Mon, 14 Aug 2006 13:23:28 +0200 Hi gmx-users! I am trying to simulate the diffusion of mannitol through a lipid bilayer with AFM pulling. Does someone have a idea, how I can calculate the diffusion coefficent from the potential of mean force? I have some references, but for different methodes like umbrella sampling. AFM pulling is identical to umbrella sampling. (note that you should pull slow enough so the system is in equilibrium) We should merge these two options into one option. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] AFM pulling
Thanks, that's good to know! Susanna From: Susanna Hug [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] AFM pulling Date: Mon, 14 Aug 2006 13:23:28 +0200 Hi gmx-users! I am trying to simulate the diffusion of mannitol through a lipid bilayer with AFM pulling. Does someone have a idea, how I can calculate the diffusion coefficent from the potential of mean force? I have some references, but for different methodes like umbrella sampling. AFM pulling is identical to umbrella sampling. (note that you should pull slow enough so the system is in equilibrium) We should merge these two options into one option. Berk. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] AFM Pulling Rate
Hello Bob, have you tried to define the initial position of the AFM-tip? It needs to be set to the position of the COM of the group you want to pull. try and add afm_init1 = x y z (x y z = position where the afm should be) to your pull.ppa. Otherwise your afmspring is extended from the beginning so much, that this extension dominates the force on the pulling group and the pullingrate is nearly irrelevant until the system relaxed. ciao Jan Hello everyone, I am using AFM pulling to drag a dna base across the surface of a graphene. I'm doing this in vaccuum. It seems that the base is pulled at the same rate no matter what value I specify in afm_rate1. Here is my pull.ppa file: runtype = afm group_1 = ssdna-ions pulldim = N N Y afm_rate1 = 0.05 afm_k1 = 100 afm_dir1 = 0 0 1 I'm using version 3.3. Does anyone know what's going on? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] AFM Pulling Rate
Hello everyone, I am using AFM pulling to drag a dna base across the surface of a graphene. I'm doing this in vaccuum. It seems that the base is pulled at the same rate no matter what value I specify in afm_rate1. Here is my pull.ppa file: runtype = afm group_1 = ssdna-ions pulldim = N N Y afm_rate1 = 0.05 afm_k1 = 100 afm_dir1 = 0 0 1 I'm using version 3.3. Does anyone know what's going on? Thanks, Bob Johnson ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] afm pulling and comm_mode
Hi again, I pretty much went about the setting up of afm pulling calculations. Still I am a little bit concern about the results. When using gmx3.2.1 and applying a Linear removal of the center of mass (i.e. translation) I see the cell unit still moving during the simulation in a direction that, looks to me, is opposite to the force I am applying. In fact, when the pulling rate is smaller, the move is not as dramatic. What am I doing wrong? I have no note that with 3.3 this doesn't happen. Did anyone experience something like that? Any tip/suggestion will be greatly appreciated Best M Marta Murcia wrote: Thanks Emily and Maik for your feed-back You both are right regarding the init vector. I happened to be the sign of it as Emily guessed. Changing the direction by doing xpull-xref, ypull -yref, zpull-zref and not xref-xpull.works fine. Thanks for the offer on the script though. Thanks Emily for claryfing my confusion on the directional vector All the best M Maik Goette wrote: Hi There seems to be something wrong with your init-vector. Ich have written a small python script, which simply calculates the vector for convenience purposes. You still need the pull- and COM-group coordinates, though. But that shouldn't be a problem. If you want it, I'll send it via mail. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Marta Murcia wrote: Emily, I just saw your answer Thanks a lot I just have another question about the unit vector describing the direction of pulling. Should it be always a unit vector (1 1 1 for example)? Should I asumme then that the direction of the pulling is the one specified by the init vector or could I used that same vector for example as afm_dir? Also, I don't know if I am doing something wrong but using afm_ini 1 1 1 and afm_dir as the vector that connects the two atoms I've chosen (the pulled and the ref) I am not able to get the spring and the pulled atom at the same coordinates at the beginning of pull.pdo file. # AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group 'm' # Nr. of pull groups 1 # Group 1 'a_13586' afmVec 1.00 1.00 1.00 AfmRate 0.02 AfmK 3000.00 # 0.003.7130005.6270005.181000 3.6940003.7320005.7120005.542000 4.895.472001 I was able to get it, though, using absolute coordinates leaving the reference group blanck (using gromac 3.3 since in 3.2.1 there is a bug on absolute coordinates) #AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group '' # Nr. of pull groups 1 # Group 1 'a_13586' afmVec 1.00 1.00 1.00 AfmRate 0.02 AfmK 3000.00 # 0.00 0.000.000.00 3.6940003.6940005.7120005.712000 4.894.89 what is wrong? am i choosing the wrong starting vector when using a reference group? (Note that I am using xref-xpull, yref-ypull, zref-zpull as afm-ini, 0.019 -0.085 0.291) Again, thanks a lot M Emily Walton wrote: Hi, Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group within a molecule can not be used? Not even as a reference group? Any group that is defined in your index file (specified with mdrun - pn pull.ndx) can be used. Look at made_ndx in the manual to learn how to add new groups. 2-Should I need to fixed the center of mass of the protein to avoid shifts? How can I do that? Would it be OK to use posre for the backbone of the protein with carrying out the pulling? It depends on what you want to do. Typically, something would need to be fixed. In ligand-protein systems, the center of mass of the protein is a reasonable choice. It was used by Grubmuller et al. in their 1996 Science paper on the unbinding of biotin-streptavidin. (Science, 271:954–5, 1996) For unraveling of proteins, one terminal atom may be fixed while the other is pulled. Fixing the center of mass of a group in the index file can be done in the .mdp file you feed to grompp. See the manual, chapter 7. 3-Should I removed all the constraints for the bonds (SHAKE, lincs)? I think this is a matter of preference. Some people do, some people don't. Again, it will depend on your system- is it stable without the constraints? The bonds that are broken with afm pulling are bonds described by non- bonded interaction terms in gromacs. These bonds
Re: [gmx-users] afm pulling
Hi There seems to be something wrong with your init-vector. Ich have written a small python script, which simply calculates the vector for convenience purposes. You still need the pull- and COM-group coordinates, though. But that shouldn't be a problem. If you want it, I'll send it via mail. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Marta Murcia wrote: Emily, I just saw your answer Thanks a lot I just have another question about the unit vector describing the direction of pulling. Should it be always a unit vector (1 1 1 for example)? Should I asumme then that the direction of the pulling is the one specified by the init vector or could I used that same vector for example as afm_dir? Also, I don't know if I am doing something wrong but using afm_ini 1 1 1 and afm_dir as the vector that connects the two atoms I've chosen (the pulled and the ref) I am not able to get the spring and the pulled atom at the same coordinates at the beginning of pull.pdo file. # AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group 'm' # Nr. of pull groups 1 # Group 1 'a_13586' afmVec 1.00 1.00 1.00 AfmRate 0.02 AfmK 3000.00 # 0.003.7130005.6270005.181000 3.6940003.7320005.7120005.542000 4.895.472001 I was able to get it, though, using absolute coordinates leaving the reference group blanck (using gromac 3.3 since in 3.2.1 there is a bug on absolute coordinates) #AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group '' # Nr. of pull groups 1 # Group 1 'a_13586' afmVec 1.00 1.00 1.00 AfmRate 0.02 AfmK 3000.00 # 0.00 0.000.000.00 3.6940003.6940005.7120005.712000 4.894.89 what is wrong? am i choosing the wrong starting vector when using a reference group? (Note that I am using xref-xpull, yref-ypull, zref-zpull as afm-ini, 0.019 -0.085 0.291) Again, thanks a lot M Emily Walton wrote: Hi, Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group within a molecule can not be used? Not even as a reference group? Any group that is defined in your index file (specified with mdrun - pn pull.ndx) can be used. Look at made_ndx in the manual to learn how to add new groups. 2-Should I need to fixed the center of mass of the protein to avoid shifts? How can I do that? Would it be OK to use posre for the backbone of the protein with carrying out the pulling? It depends on what you want to do. Typically, something would need to be fixed. In ligand-protein systems, the center of mass of the protein is a reasonable choice. It was used by Grubmuller et al. in their 1996 Science paper on the unbinding of biotin-streptavidin. (Science, 271:954–5, 1996) For unraveling of proteins, one terminal atom may be fixed while the other is pulled. Fixing the center of mass of a group in the index file can be done in the .mdp file you feed to grompp. See the manual, chapter 7. 3-Should I removed all the constraints for the bonds (SHAKE, lincs)? I think this is a matter of preference. Some people do, some people don't. Again, it will depend on your system- is it stable without the constraints? The bonds that are broken with afm pulling are bonds described by non- bonded interaction terms in gromacs. These bonds wouldn't be constrained by shake or lincs anyway, so the presence or absence of constrains should have a minimal effect on the simulation results. 4-once I have the pull.pdo the calculation of the applied force will be F= K*(zspring -zgroup) (assuming I am pulling in the z direction)? Yes. The spring is an ideal spring, so force is k*(extension). The extension can be calculated from the pull.pdo file. -Emily Walton___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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.ph p ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post?
Re: [gmx-users] afm pulling
Thanks Emily and Maik for your feed-back You both are right regarding the init vector. I happened to be the sign of it as Emily guessed. Changing the direction by doing xpull-xref, ypull -yref, zpull-zref and not xref-xpull.works fine. Thanks for the offer on the script though. Thanks Emily for claryfing my confusion on the directional vector All the best M Maik Goette wrote: Hi There seems to be something wrong with your init-vector. Ich have written a small python script, which simply calculates the vector for convenience purposes. You still need the pull- and COM-group coordinates, though. But that shouldn't be a problem. If you want it, I'll send it via mail. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Marta Murcia wrote: Emily, I just saw your answer Thanks a lot I just have another question about the unit vector describing the direction of pulling. Should it be always a unit vector (1 1 1 for example)? Should I asumme then that the direction of the pulling is the one specified by the init vector or could I used that same vector for example as afm_dir? Also, I don't know if I am doing something wrong but using afm_ini 1 1 1 and afm_dir as the vector that connects the two atoms I've chosen (the pulled and the ref) I am not able to get the spring and the pulled atom at the same coordinates at the beginning of pull.pdo file. # AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group 'm' # Nr. of pull groups 1 # Group 1 'a_13586' afmVec 1.00 1.00 1.00 AfmRate 0.02 AfmK 3000.00 # 0.003.7130005.6270005.181000 3.6940003.7320005.7120005.542000 4.895.472001 I was able to get it, though, using absolute coordinates leaving the reference group blanck (using gromac 3.3 since in 3.2.1 there is a bug on absolute coordinates) #AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group '' # Nr. of pull groups 1 # Group 1 'a_13586' afmVec 1.00 1.00 1.00 AfmRate 0.02 AfmK 3000.00 # 0.00 0.000.000.00 3.6940003.6940005.7120005.712000 4.894.89 what is wrong? am i choosing the wrong starting vector when using a reference group? (Note that I am using xref-xpull, yref-ypull, zref-zpull as afm-ini, 0.019 -0.085 0.291) Again, thanks a lot M Emily Walton wrote: Hi, Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group within a molecule can not be used? Not even as a reference group? Any group that is defined in your index file (specified with mdrun - pn pull.ndx) can be used. Look at made_ndx in the manual to learn how to add new groups. 2-Should I need to fixed the center of mass of the protein to avoid shifts? How can I do that? Would it be OK to use posre for the backbone of the protein with carrying out the pulling? It depends on what you want to do. Typically, something would need to be fixed. In ligand-protein systems, the center of mass of the protein is a reasonable choice. It was used by Grubmuller et al. in their 1996 Science paper on the unbinding of biotin-streptavidin. (Science, 271:954–5, 1996) For unraveling of proteins, one terminal atom may be fixed while the other is pulled. Fixing the center of mass of a group in the index file can be done in the .mdp file you feed to grompp. See the manual, chapter 7. 3-Should I removed all the constraints for the bonds (SHAKE, lincs)? I think this is a matter of preference. Some people do, some people don't. Again, it will depend on your system- is it stable without the constraints? The bonds that are broken with afm pulling are bonds described by non- bonded interaction terms in gromacs. These bonds wouldn't be constrained by shake or lincs anyway, so the presence or absence of constrains should have a minimal effect on the simulation results. 4-once I have the pull.pdo the calculation of the applied force will be F= K*(zspring -zgroup) (assuming I am pulling in the z direction)? Yes. The spring is an ideal spring, so force is k*(extension). The extension can be calculated from the pull.pdo file. -Emily Walton___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to
Re: [gmx-users] afm pulling
Emily Walton wrote: afm_init describes only the initial position of the spring. afm_dir describes how that position will change with time. You can normalize afm_init and use it for afm_dir if you want- you'd be pulling along the direction connecting the com of your reference and pull groups. One last thing Emily, should be afm_dir vector be referenced to the reference group as origin as well as afm_init is, or kept the direction relative to 0,0,0 origin of the system? Thanks M ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] afm pulling
Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group within a molecule can not be used? Not even as a reference group? 2-Should I need to fixed the center of mass of the protein to avoid shifts? How can I do that? Would it be OK to use posre for the backbone of the protein with carrying out the pulling? 3-Should I removed all the constraints for the bonds (SHAKE, lincs)? 4-once I have the pull.pdo the calculation of the applied force will be F= K*(zspring -zgroup) (assuming I am pulling in the z direction)? Thanks in advance for your help. Appreciated! Best M ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] afm pulling
Hi, Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group within a molecule can not be used? Not even as a reference group? Any group that is defined in your index file (specified with mdrun - pn pull.ndx) can be used. Look at made_ndx in the manual to learn how to add new groups. 2-Should I need to fixed the center of mass of the protein to avoid shifts? How can I do that? Would it be OK to use posre for the backbone of the protein with carrying out the pulling? It depends on what you want to do. Typically, something would need to be fixed. In ligand-protein systems, the center of mass of the protein is a reasonable choice. It was used by Grubmuller et al. in their 1996 Science paper on the unbinding of biotin-streptavidin. (Science, 271:954–5, 1996) For unraveling of proteins, one terminal atom may be fixed while the other is pulled. Fixing the center of mass of a group in the index file can be done in the .mdp file you feed to grompp. See the manual, chapter 7. 3-Should I removed all the constraints for the bonds (SHAKE, lincs)? I think this is a matter of preference. Some people do, some people don't. Again, it will depend on your system- is it stable without the constraints? The bonds that are broken with afm pulling are bonds described by non- bonded interaction terms in gromacs. These bonds wouldn't be constrained by shake or lincs anyway, so the presence or absence of constrains should have a minimal effect on the simulation results. 4-once I have the pull.pdo the calculation of the applied force will be F= K*(zspring -zgroup) (assuming I am pulling in the z direction)? Yes. The spring is an ideal spring, so force is k*(extension). The extension can be calculated from the pull.pdo file. -Emily Walton___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] AFM pulling
Hi all, I am a bit confused about some points on the manual (section 6.1, manual 3.2). I f i define two groups: one that will be pulled and the other as reference group; then the force constant and the rate, must i define also the afm_dir and the afm_unit? In my mind, if i define two groups (centers) in the space, they will define a vector where the spring will be placed and then I'll set also the strenght of pulling and its movement (rate). Could someone give me some hints or comments about? Many thanks Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
