[gmx-users] elastic network model - atoms movement
Hi all, I want to build elastic network model using gromacs. I consider only c-alpha atoms and only bond stretching term contributes to towards potential energy. Bonds are connected between atoms present with in certain cut-off distance(modified topology accordingly). When I run md the atoms are not present at the equillibrium distance but moving very far distances , in different directions. I do not want to use constraints. How can i avoid this? 2) Has anyone built elastic network model in gromacs? Please suggest me a way, Thank you in advance, Mohan. -- 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] elastic network model - normal mode analysis
On 23/09/2012 5:22 PM, mohan maruthi sena wrote: Hi all, I want to do normal mode analysis for a protein using elastic network model containing 691 residues. I consider only c-alpha atoms connected by a spring constant of 81600 kj/nm2. When I do normal mode analysis I get the following error : Maximum force: 6.30230e+02 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. Finished step 691 out of 691 I have minimised the structure , still i get the same error. I use in gromacs 4.5.5 double precision for these simulations. When I load the trajectory eigen.trr in vmd(to see normal modes) , I could see the protein far away and all atoms overlapped. I use the following .mdp file parameters as input ; RUN CONTROL PARAMETERS integrator = nm dt = 0.002 ; time step (ps) nsteps = 100 ; number of steps ; OUTPUT CONTROL OPTIONS nstenergy= 500 nstxout = 500 nstvout = 500 nstfout = 500 energygrps = System ; NEIGHBORSEARCHING PARAMETERS nstlist = 0 #Frequency to update neighbourlist pbc = no comm_mode = ANGULAR ; OPTIONS FOR ELECTROSTATICS AND VDW ; Temperature coupling tcoupl = v-rescale ; Couple temperature to external heat bath according to Berendsen method tc-grps = System ;Non-Protein ; Use separate heat baths for Protein and Non-Protein groups tau_t= 0.2 ;0.2 ; Coupling time constant, controlling strength of coupling ref_t= 300; Temperature of heat bath ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; Assign velocities to particles by taking them randomly from a Maxwell distribution gen_temp = 300.0 ; Temperature to generate corresponding Maxwell distribution gen_seed = ; Seed for (semi) random number generation. Different numbers give different sets of velocities ; OPTIONS FOR BONDS constraints = none ; No constraints except for those defined explicitly in the topology refcoord_scaling = com Please suggest me a way to rectify this error. You're doing something wrong in the construction of your model. Find a toy example in the literature that you can attempt to copy so that you know you know how to walk before you try to run. Failing that, construct some geometric solid that should be stable, like a tetragonal pyramid, or something. Until you can do that, worrying about a protein is a waste of time. The strength of your forces, temperature and size of your time step are all closely interlinked if you want the integration to do something sensible, and probably you're inventing all of them at the moment. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Elastic Network Model -harmonic pot
Hi all, I am trying to build an elastic network model using only C-alpha atoms . Potential energy function contains only bond stretching energy term rest like angle,dihedral and non bonded are not included. I use bond function type(f.tp = 6) ,i.e. is harmonic bond potential . The problem is that atoms connected by harmonic potential are rotating . I do not want to use any constraints. How can I fix this ? Thanks in advance, -- Mohan -- 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] Elastic network model
Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 3 1 1 5.10184956658 61.9 3 2 1 3.69916125628 61.9 4 1 1 4.19781502689 61.9 4 2 1 5.90237528458 61.9 4 3 1 3.92569102197 61.9 5 1 1 5.30324730708 61.9 5 3 1 5.269426249661.9 5 4 1 3.83092403997 61.9 6 3 1 4.07288043036 61.9 6 4 1 5.48720921781 61.9 6 5 1 3.71358990735 61.9 7 3 1 5.51608248669 61.9 7 6 1 3.868286571661.9 8 7 1 3.804772135161.9 9 8 1 3.81975719124 61.9 10 9 1 3.72026195314 61.9 11 10 1 3.76893910802 61.9 12 11 1 3.812386522961.9 13 12 1 3.78850801768 61.9 14 13 1 3.69171193351 61.9 15 13 1 5.42834818338 61.9 15 14 1 3.83449357804 61.9 16 13 1 5.10757946585 61.9 16 15 1 3.83922544272 61.9 17 11 1 5.71881902144 61.9 17 12 1 4.83263696133 61.9 17 13 1 5.48196032456 61.9 The above one is part of topology file. I have 372 residues in my protein. when i run equilibration i got the following error A list of missing interactions: Bond . of 1027 missing 1 --- Program mdrun_d, VERSION 4.5.5 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. None of the interactions are repeated multiple times, when i check the log file the following error is written Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Bond. of 1027 missing 1 --- Program mdrun_d, VERSION 4.5.5 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Error Can you suggest me what does this error mean . Is the topology correct (built) with respect to elastic network model. Thank you, Mohan On Thu, Aug 30, 2012 at 5:58 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi , Thank you very much .I will take all these factors in to account while building the model. Thank you, Mohan. On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 30/08/2012 10:17 PM, Mark Abraham wrote: On 30/08/2012 10:02 PM, mohan maruthi sena wrote: Hi, I am going through it , i will understand it and try to build the topology. Fundamentally, harmonic bonds do not serve your purpose, since you need an interaction that is harmonic in the change in distance, not harmonic in the distance. Hence your problems with collapsing systems. As such, you want to look at using distance restraints, rather than [bonds]. On second thoughts, a sufficient network of harmonic bonds can suffice, but you need to embed the distance in the topology. [distance_restraints] are just easier because you can let the initial structure determine the equilibrium position. (Unless you don't want that) Mark Mark Thank you, Mohan On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, You need to check chapter 5 of the gromacs manual to understand the topology format to write. You probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the specifications in the manual. Cheers, Tsjerk On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi, Thanks for a quick reply. In these models we use a distance cut-off method. Around a particular atom we take a cut-off distance and connect to all those atoms which fall in the cut-off. I do not understand, how to connect this atoms with the other atoms falling in cut-off distance. I have written a script to know the atom numbers falling with in cut-off distance. I replace bonds section in topology with these atom connectivity information that i got from script. Is this method correct or else please suggest me a way.Can you elaborate on write a script to generate .top Thank you very much, Mohan On
Re: [gmx-users] Elastic network model
On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 Less than 6 Angstrom ??? You need to read the topology chapter of the manual again. And then again. It will save you lots of time later. Hint: some units are wrong. Good luck! Bogdan -- 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] Elastic network model
GROMACS uses nm as the unit of length, so this is 38 Angstroms, shouldn't be a problem. On 2012-08-31, at 2:23 PM, Bogdan Costescu bcoste...@gmail.com wrote: On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 Less than 6 Angstrom ??? You need to read the topology chapter of the manual again. And then again. It will save you lots of time later. Hint: some units are wrong. Good luck! Bogdan -- 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] Elastic network model
On 1/09/2012 4:42 AM, mohan maruthi sena wrote: Hi all, I have built topology for elastic network as follows(the atoms which fall with in a distance less than 6 angtroms are bonded). [bonds] ;aiaj funct bo kb 2 1 1 3.80444752888 61.9 3 1 1 5.10184956658 61.9 3 2 1 3.69916125628 61.9 4 1 1 4.19781502689 61.9 4 2 1 5.90237528458 61.9 4 3 1 3.92569102197 61.9 5 1 1 5.30324730708 61.9 5 3 1 5.269426249661.9 5 4 1 3.83092403997 61.9 6 3 1 4.07288043036 61.9 6 4 1 5.48720921781 61.9 6 5 1 3.71358990735 61.9 7 3 1 5.51608248669 61.9 7 6 1 3.868286571661.9 8 7 1 3.804772135161.9 9 8 1 3.81975719124 61.9 10 9 1 3.72026195314 61.9 11 10 1 3.76893910802 61.9 12 11 1 3.812386522961.9 13 12 1 3.78850801768 61.9 14 13 1 3.69171193351 61.9 15 13 1 5.42834818338 61.9 15 14 1 3.83449357804 61.9 16 13 1 5.10757946585 61.9 16 15 1 3.83922544272 61.9 17 11 1 5.71881902144 61.9 17 12 1 4.83263696133 61.9 17 13 1 5.48196032456 61.9 The above one is part of topology file. I have 372 residues in my protein. when i run equilibration i got the following error A list of missing interactions: Bond . of 1027 missing 1 --- Program mdrun_d, VERSION 4.5.5 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. None of the interactions are repeated multiple times, when i check the log file the following error is written Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Bond. of 1027 missing 1 --- Program mdrun_d, VERSION 4.5.5 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Error Can you suggest me what does this error mean . Is the topology correct (built) with respect to elastic network model. It means your system is http://www.gromacs.org/Documentation/Terminology/Blowing_Up. Maybe your velocities are far too large for your tiny bond stiffness constants, or your integration step was too large, or probably a dozen other things we can only guess at because we don't know your initial configuration or your .mdp file contents. If you're just inventing stuff on your own, then I suggest you find an actual elastic network model of which someone else has already published a dynamical model, and work out how to implement that, instead of hoping someone will tell you how an actual elastic network model works. Only then do you have some basis for seeking to do something novel. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Elastic network model
Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- 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] Elastic network model
Hi Mohan, Elastic network modeling consists of building a Hessian matrix based on the distances. That matrix is then diagonalized and the modes are further investigated. You could write a script to generate a .top file with a [ bonds ] section, capturing the elastic bonds, and then use Gromacs to generate the Hessian using the nm integrator. But that seems more trouble than it's worth. If you think of building such a model and then simulate it using an md integrator, be warned that these models are very incomplete and are intended to only capture the tangents around the starting structure. Hope it helps, Tsjerk On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Elastic network model
Hi, Thanks for a quick reply. In these models we use a distance cut-off method. Around a particular atom we take a cut-off distance and connect to all those atoms which fall in the cut-off. I do not understand, how to connect this atoms with the other atoms falling in cut-off distance. I have written a script to know the atom numbers falling with in cut-off distance. I replace bonds section in topology with these atom connectivity information that i got from script. Is this method correct or else please suggest me a way.Can you elaborate on write a script to generate .top Thank you very much, Mohan On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, Elastic network modeling consists of building a Hessian matrix based on the distances. That matrix is then diagonalized and the modes are further investigated. You could write a script to generate a .top file with a [ bonds ] section, capturing the elastic bonds, and then use Gromacs to generate the Hessian using the nm integrator. But that seems more trouble than it's worth. If you think of building such a model and then simulate it using an md integrator, be warned that these models are very incomplete and are intended to only capture the tangents around the starting structure. Hope it helps, Tsjerk On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Elastic network model
Hi Mohan, You need to check chapter 5 of the gromacs manual to understand the topology format to write. You probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the specifications in the manual. Cheers, Tsjerk On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi, Thanks for a quick reply. In these models we use a distance cut-off method. Around a particular atom we take a cut-off distance and connect to all those atoms which fall in the cut-off. I do not understand, how to connect this atoms with the other atoms falling in cut-off distance. I have written a script to know the atom numbers falling with in cut-off distance. I replace bonds section in topology with these atom connectivity information that i got from script. Is this method correct or else please suggest me a way.Can you elaborate on write a script to generate .top Thank you very much, Mohan On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, Elastic network modeling consists of building a Hessian matrix based on the distances. That matrix is then diagonalized and the modes are further investigated. You could write a script to generate a .top file with a [ bonds ] section, capturing the elastic bonds, and then use Gromacs to generate the Hessian using the nm integrator. But that seems more trouble than it's worth. If you think of building such a model and then simulate it using an md integrator, be warned that these models are very incomplete and are intended to only capture the tangents around the starting structure. Hope it helps, Tsjerk On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Elastic network model
Hi, I am going through it , i will understand it and try to build the topology. Thank you, Mohan On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, You need to check chapter 5 of the gromacs manual to understand the topology format to write. You probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the specifications in the manual. Cheers, Tsjerk On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi, Thanks for a quick reply. In these models we use a distance cut-off method. Around a particular atom we take a cut-off distance and connect to all those atoms which fall in the cut-off. I do not understand, how to connect this atoms with the other atoms falling in cut-off distance. I have written a script to know the atom numbers falling with in cut-off distance. I replace bonds section in topology with these atom connectivity information that i got from script. Is this method correct or else please suggest me a way.Can you elaborate on write a script to generate .top Thank you very much, Mohan On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, Elastic network modeling consists of building a Hessian matrix based on the distances. That matrix is then diagonalized and the modes are further investigated. You could write a script to generate a .top file with a [ bonds ] section, capturing the elastic bonds, and then use Gromacs to generate the Hessian using the nm integrator. But that seems more trouble than it's worth. If you think of building such a model and then simulate it using an md integrator, be warned that these models are very incomplete and are intended to only capture the tangents around the starting structure. Hope it helps, Tsjerk On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Elastic network model
On 30/08/2012 10:02 PM, mohan maruthi sena wrote: Hi, I am going through it , i will understand it and try to build the topology. Fundamentally, harmonic bonds do not serve your purpose, since you need an interaction that is harmonic in the change in distance, not harmonic in the distance. Hence your problems with collapsing systems. As such, you want to look at using distance restraints, rather than [bonds]. Mark Thank you, Mohan On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, You need to check chapter 5 of the gromacs manual to understand the topology format to write. You probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the specifications in the manual. Cheers, Tsjerk On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi, Thanks for a quick reply. In these models we use a distance cut-off method. Around a particular atom we take a cut-off distance and connect to all those atoms which fall in the cut-off. I do not understand, how to connect this atoms with the other atoms falling in cut-off distance. I have written a script to know the atom numbers falling with in cut-off distance. I replace bonds section in topology with these atom connectivity information that i got from script. Is this method correct or else please suggest me a way.Can you elaborate on write a script to generate .top Thank you very much, Mohan On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, Elastic network modeling consists of building a Hessian matrix based on the distances. That matrix is then diagonalized and the modes are further investigated. You could write a script to generate a .top file with a [ bonds ] section, capturing the elastic bonds, and then use Gromacs to generate the Hessian using the nm integrator. But that seems more trouble than it's worth. If you think of building such a model and then simulate it using an md integrator, be warned that these models are very incomplete and are intended to only capture the tangents around the starting structure. Hope it helps, Tsjerk On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Elastic network model
On 30/08/2012 10:17 PM, Mark Abraham wrote: On 30/08/2012 10:02 PM, mohan maruthi sena wrote: Hi, I am going through it , i will understand it and try to build the topology. Fundamentally, harmonic bonds do not serve your purpose, since you need an interaction that is harmonic in the change in distance, not harmonic in the distance. Hence your problems with collapsing systems. As such, you want to look at using distance restraints, rather than [bonds]. On second thoughts, a sufficient network of harmonic bonds can suffice, but you need to embed the distance in the topology. [distance_restraints] are just easier because you can let the initial structure determine the equilibrium position. (Unless you don't want that) Mark Mark Thank you, Mohan On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, You need to check chapter 5 of the gromacs manual to understand the topology format to write. You probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the specifications in the manual. Cheers, Tsjerk On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi, Thanks for a quick reply. In these models we use a distance cut-off method. Around a particular atom we take a cut-off distance and connect to all those atoms which fall in the cut-off. I do not understand, how to connect this atoms with the other atoms falling in cut-off distance. I have written a script to know the atom numbers falling with in cut-off distance. I replace bonds section in topology with these atom connectivity information that i got from script. Is this method correct or else please suggest me a way.Can you elaborate on write a script to generate .top Thank you very much, Mohan On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, Elastic network modeling consists of building a Hessian matrix based on the distances. That matrix is then diagonalized and the modes are further investigated. You could write a script to generate a .top file with a [ bonds ] section, capturing the elastic bonds, and then use Gromacs to generate the Hessian using the nm integrator. But that seems more trouble than it's worth. If you think of building such a model and then simulate it using an md integrator, be warned that these models are very incomplete and are intended to only capture the tangents around the starting structure. Hope it helps, Tsjerk On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
Re: [gmx-users] Elastic network model
Hi , Thank you very much .I will take all these factors in to account while building the model. Thank you, Mohan. On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 30/08/2012 10:17 PM, Mark Abraham wrote: On 30/08/2012 10:02 PM, mohan maruthi sena wrote: Hi, I am going through it , i will understand it and try to build the topology. Fundamentally, harmonic bonds do not serve your purpose, since you need an interaction that is harmonic in the change in distance, not harmonic in the distance. Hence your problems with collapsing systems. As such, you want to look at using distance restraints, rather than [bonds]. On second thoughts, a sufficient network of harmonic bonds can suffice, but you need to embed the distance in the topology. [distance_restraints] are just easier because you can let the initial structure determine the equilibrium position. (Unless you don't want that) Mark Mark Thank you, Mohan On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, You need to check chapter 5 of the gromacs manual to understand the topology format to write. You probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the specifications in the manual. Cheers, Tsjerk On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi, Thanks for a quick reply. In these models we use a distance cut-off method. Around a particular atom we take a cut-off distance and connect to all those atoms which fall in the cut-off. I do not understand, how to connect this atoms with the other atoms falling in cut-off distance. I have written a script to know the atom numbers falling with in cut-off distance. I replace bonds section in topology with these atom connectivity information that i got from script. Is this method correct or else please suggest me a way.Can you elaborate on write a script to generate .top Thank you very much, Mohan On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Mohan, Elastic network modeling consists of building a Hessian matrix based on the distances. That matrix is then diagonalized and the modes are further investigated. You could write a script to generate a .top file with a [ bonds ] section, capturing the elastic bonds, and then use Gromacs to generate the Hessian using the nm integrator. But that seems more trouble than it's worth. If you think of building such a model and then simulate it using an md integrator, be warned that these models are very incomplete and are intended to only capture the tangents around the starting structure. Hope it helps, Tsjerk On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, Can any one suggest me how to build elastic network model in gromacs. Thanks, Mohan -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
Re: [gmx-users] Elastic network model -building
There is no script generating an elastic network in Gromacs. You could use the script that we developed in the context of the Martini CG model (cgmartini.nl) but it would be certainly easier for you to simply write a script that would rad the Clapha coordinates and define the ones that are within a cut-off distance of your choice and then write a list of bonds that you could add to a gromacs topology file ... On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote: Hi all, I want to build elastic network model for a protein. To build an Elastic network model , I consider only C-alpha atoms of the protein. I want to make c-alpha atoms connect(make bond) with all the other c-alpha atoms , if it falls within certain cut-off distance. How can i do this? Please suggest me a way, Thanks, Mohan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Elastic network model -building
Hi, Thanks for your reply. I have written a script which gives the atoms with in certain cut-off distance from specified atom. I have added this to topology , the problem is that it creates topology from pdb but not the other way. I use first pdb2gmx -f pdb -o gro -p top (command to generate gro,top). I use this topology file and add the bonds in this and use this topology for further use. Is this correct,?,but still i could not find bonds with other atoms when i load it in vmd. Please suggest me a way. Thanks, Mohan On Mon, Aug 27, 2012 at 10:29 PM, XAvier Periole x.peri...@rug.nl wrote: There is no script generating an elastic network in Gromacs. You could use the script that we developed in the context of the Martini CG model (cgmartini.nl) but it would be certainly easier for you to simply write a script that would rad the Clapha coordinates and define the ones that are within a cut-off distance of your choice and then write a list of bonds that you could add to a gromacs topology file ... On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote: Hi all, I want to build elastic network model for a protein. To build an Elastic network model , I consider only C-alpha atoms of the protein. I want to make c-alpha atoms connect(make bond) with all the other c-alpha atoms , if it falls within certain cut-off distance. How can i do this? Please suggest me a way, Thanks, Mohan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 thewww 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] Elastic network model -building
On Aug 27, 2012, at 7:14 PM, mohan maruthi sena wrote: Hi, Thanks for your reply. I have written a script which gives the atoms with in certain cut-off distance from specified atom. I have added this to topology , the problem is that it creates topology from pdb but not the other way. Not clear what the other way around is! I use first pdb2gmx -f pdb -o gro -p top (command to generate gro,top). I use this topology file and add the bonds in this and use this topology for further use. Is this correct,? I have no idea! It depends what you want to do! Doing like you describe you add a elastic network to a atomistic description ... if this is not the objective do something that would follow your idea! ,but still i could not find bonds with other atoms when i load it in vmd. Please suggest me a way. VMD defines default bonds according to their distances in the structure you give. So between Calpha the distance is about 0.38 nm ... if you use a dynamic bond description in VMD and select the Calphas ... a cutoff of 4.0 would show you the connections. Thanks, Mohan On Mon, Aug 27, 2012 at 10:29 PM, XAvier Periole x.peri...@rug.nl wrote: There is no script generating an elastic network in Gromacs. You could use the script that we developed in the context of the Martini CG model (cgmartini.nl) but it would be certainly easier for you to simply write a script that would rad the Clapha coordinates and define the ones that are within a cut-off distance of your choice and then write a list of bonds that you could add to a gromacs topology file ... On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote: Hi all, I want to build elastic network model for a protein. To build an Elastic network model , I consider only C-alpha atoms of the protein. I want to make c-alpha atoms connect(make bond) with all the other c-alpha atoms , if it falls within certain cut-off distance. How can i do this? Please suggest me a way, Thanks, Mohan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 thewww 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
[gmx-users] Elastic network model -building
Hi all, I want to build elastic network model for a protein. To build an Elastic network model , I consider only C-alpha atoms of the protein. I want to make c-alpha atoms connect(make bond) with all the other c-alpha atoms , if it falls within certain cut-off distance. How can i do this? Please suggest me a way, Thanks, Mohan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Elastic network model -gromacs
Hi all , Can any one suggest me how to build elastic network model in gromacs ( any literature,tutorial kind). Thanks in advance, K.Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] elastic network model -protein contracting
Hi all, I want to prepare a basic elastic network model (tirion model) of protein. For this i have taken only C-alpha atoms of the protein and considered only streching potential(k.(b-b0)^2)) and removed rest of angle,dihedral,non bonded interactions. I have mentioned a bond between C-alpha and C-alpha in ffbonded.itp file with equilibrium distance 0.39 nm and force constant of 96400 kj/nm2 . I don't performed any minimisation ,just done equilibration and production. When i load final trajectory file(after production run) the protein contracts after first frame ,some of the atoms are over one another overlapping one over the other. Please help me to solve this problem. Thanks in advance, Mohan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] elastic network model -protein contracting
On 22/08/2012 1:06 PM, mohan maruthi sena wrote: Hi all, I want to prepare a basic elastic network model (tirion model) of protein. For this i have taken only C-alpha atoms of the protein and considered only streching potential(k.(b-b0)^2)) and removed rest of angle,dihedral,non bonded interactions. I have mentioned a bond between C-alpha and C-alpha in ffbonded.itp file with equilibrium distance 0.39 nm and force constant of 96400 kj/nm2 . I don't performed any minimisation ,just done equilibration and production. When i load final trajectory file(after production run) the protein contracts after first frame ,some of the atoms are over one another overlapping one over the other. Please help me to solve this problem. Your model has no way to prevent overlap. You need to fix the model. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Elastic Network Model
On Mon, Mar 30, 2009 at 3:23 PM, Joshua Adelman jadel...@berkeley.eduwrote: I am interested in potentially using gromacs to do some calculations on an C-alpha based elastic network model of the protein that I'm working on. I'm curious if other users have done similar types of calculations, and if so, what protocol you used. I realize that there are a lot of webservers out there that do this calculation, but I want to be able to use a heterogeneous network of spring constants, and have a bit more flexibility than many of them allow. Gromacs seemed like it might be a good option for tackling this problem since it can calculate the Hessian and generate the normal modes from an arbitrary force field. it also had a bunch of nice analyses tools available as well. We use the ASN server from Ivet Bahar's group and get nice results. Right now I am looking for suggestions on how to explicitly turn off all non-bonded interactions (the only FF terms are bonded terms). Define the atom types in your top file, instead of #include ff***.itp and set the LJ and Q's to zero or set nrexcl to then the number of atoms (not exactly sure what this will do but you can give it a try) Is the best option to use energygrp excl? Any other useful suggestions for using gromacs for this purpose would also be appreciated. Josh ___ 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 thewww 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Elastic Network Model
I am interested in potentially using gromacs to do some calculations on an C-alpha based elastic network model of the protein that I'm working on. I'm curious if other users have done similar types of calculations, and if so, what protocol you used. I realize that there are a lot of webservers out there that do this calculation, but I want to be able to use a heterogeneous network of spring constants, and have a bit more flexibility than many of them allow. Gromacs seemed like it might be a good option for tackling this problem since it can calculate the Hessian and generate the normal modes from an arbitrary force field. it also had a bunch of nice analyses tools available as well. Right now I am looking for suggestions on how to explicitly turn off all non-bonded interactions (the only FF terms are bonded terms). Is the best option to use energygrp excl? Any other useful suggestions for using gromacs for this purpose would also be appreciated. Josh ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
