[gmx-users] Persistence length of whole DNA molecule
Hi all, I want to calculate the persistence length of whole DNA molecule. I know that we can calculate it by using option g_polystat -f .trr -p p.xvg , but I am not able to figure out what set of of atoms I have to select while making the index, so that I could get persistence length of whole DNA molecule. I have tried by giving backbone atom index for calculation but not getting the correct values ? Please suggest me what atom index I should select which can include helical axis information while calculating the persistence length. Thanks regards, 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] Persistence length calculation using g_polystat
Hello Sir, Thank you very much for a reply. I have selected following atoms P, C5',C4',C3' atoms to estimate persistence length. I want to find persistence length of whole dna, can you please elaborate on , how to calculate persistence length of whole dna using helical axis of the dna? Thanks regards, Mohan On Mon, Jul 22, 2013 at 3:35 PM, rajendra kumar rjd...@gmail.com wrote: Which group of atoms you have taken for the persistence length? g_polystat requires a group of atoms which are consecutively bonded in polymer main-chain. You should take only backbone atoms of one strand of the DNA. But, it does not give the persistence length for the whole DNA. I guess, to estimate persistence length of whole DNA, you have to calculate it for helical axis of the DNA. With best regards, Rajendra || |* Rajendra Kumar *| | PhD Student| | Max Planck Institute for Biophysical Chemistryhttp://www.mpibpc.mpg.de/english/start/index.php | | Theoretical and Computational Biophysicshttp://www.mpibpc.mpg.de/home/grubmueller/index.html, | | Am Fassberg 11, 37077 Goettingen, Germany | | Tel.: +49 551 201 2304| || On Sun, Jul 21, 2013 at 11:27 PM, Mohan maruthi sena maruthi.s...@gmail.com wrote: Dear gmx users, I would like to calculate persistence length of DNA using gromacs command g_polystat . The out put file of persists.xvg contains persistence length in number of bonds and it shows that the average persistence length = 4.3 bonds. How can we convert no of bonds in to length(nm)?. Please suggest me a way to solve this. Thanks for a reply in advance, With regards, 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 -- 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] Persistence length calculation using g_polystat
Dear gmx users, I would like to calculate persistence length of DNA using gromacs command g_polystat . The out put file of persists.xvg contains persistence length in number of bonds and it shows that the average persistence length = 4.3 bonds. How can we convert no of bonds in to length(nm)?. Please suggest me a way to solve this. Thanks for a reply in advance, With regards, 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] User-define non bonded table
Hi Neumann,
You can use tabulated potential option in
gromacs. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
Thanks,
Mohan
On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.comwrote:
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish to set
it up for all atoms with same potential. Is there any example of the table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
How can I tell gromacs to use it for all interactions?
Thanks
Steven
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[gmx-users] How to choose bd_fric value in brownian dynamics
Hi all, I want to perform brownian dynamics simulations using gromacs 4.5.5 for a system containing protein in water. What is the basis to select the bd_fric value for this system. I came to know through previous posts that a value of 3000 would be fine for a time step less than 4fs. My question is on what basis we choose the value for bd_fric ? How does high bd_fric value impact a simulation when compared to slow bd_fric value ? Thanks for a reply 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] How to choose bd_fric value in brownian dynamics
Hello Sir , Thanks for your quick reply. I have used bd_fric =0 and then my simulation is blowing up. I have used a time step of 0.002ps, Hence i thought if i can use some other value rather than zero but I do not know which value to use. Can you suggest any general value for protein water simulations. Thanks, Mohan On Wed, May 29, 2013 at 4:46 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: According to my understanding, setting friction coefficient is quite a personal thing. The higher is bd-fric, the smaller are velocities. Why not to set bd-fric = 0 in order to start with? See manual for details of how this trick works. Dr. Vitaly Chaban On Wed, May 29, 2013 at 11:48 AM, Mohan maruthi sena maruthi.s...@gmail.com wrote: Hi all, I want to perform brownian dynamics simulations using gromacs 4.5.5 for a system containing protein in water. What is the basis to select the bd_fric value for this system. I came to know through previous posts that a value of 3000 would be fine for a time step less than 4fs. My question is on what basis we choose the value for bd_fric ? How does high bd_fric value impact a simulation when compared to slow bd_fric value ? Thanks for a reply 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 -- 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] surrounding a peptide by ions of magnesium
Hi , Thanks for a quick reply. Sorry for not being clear, I want to surround the peptide with just ions(sodium). How can I do this? Thanks, Mohan On Thu, May 2, 2013 at 4:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 12:38 AM, Mohan maruthi sena wrote: Hi all, I have system consisting of a peptide(alpha-helix), I want the peptide to be surrounded by magnesium ions(instead of water). How can i do this gromacs? How can I find the concentration of magnesium ions. just like in solution we have 0.5 Molar Mg+2 solution, My question how can find concentration by increasing number of ions. I don't fully understand what you're trying to do, especially in the absence of solvent, but I'll venture some simple advice. Concentration is just the number of moles per unit volume. Simple unit conversion exercises will tell you how many ions are needed to achieve whatever target concentration you're looking for. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] surrounding a peptide by ions of magnesium
Hi all, I have system consisting of a peptide(alpha-helix), I want the peptide to be surrounded by magnesium ions(instead of water). How can i do this gromacs? How can I find the concentration of magnesium ions. just like in solution we have 0.5 Molar Mg+2 solution, My question how can find concentration by increasing number of ions. Thanks for a reply 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
[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
[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
[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, 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, 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
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
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
[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] Topology- make bonds with certain cut-off distance
Hi all, I want build a toplogy for a protein , for which , each and every atom has to make bonds with other atoms with in certain specified cut-off distance. How can i do this ? Please suggest me a way, 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] Topology- make bonds with certain cut-off distance
Hi , Thanks for your reply. I actually want to build an elastic network model (ENM) for Protein containing 372 residues. According to literature, ENM model only considers C-alpha atoms of protein and discards rest of the atoms.The potential only considers bonded term only. It does not contain angle,dihedral or non-bonded term. To build an ENM model the specified atom makes bond with all other atoms with certain cutoff distance. I consider the distance between two c-alpha atoms is 0.38nm and force constant of 69.1 kj/(nm)2.I have written a code which gives the number of atoms around a particular atom with in certain cut-off distance, With this i will know what are the atoms that are needed to connect a particular atom.I have generated .gro and .top files using pdb2gmx command . After generating topology file , I replace bonds section with the connectivity information i get from code. The next steps are equilibration and production. I am not sure whether it takes connectivity information from topology or not. If it is not then how can i mention it forms bonds with in certain distance . Finally , if i run the simulation with all the above mentioned steps and load the trajectory in vmd , the protien gets contracted after first step. Thanks, Mohan On Sat, Aug 25, 2012 at 3:43 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, In case you want the bonds to be dynamic I think the only way is to use tabulated interactions. A bit tedious to set up, but doable. Note that this will NOT emulate angles or dihedrals, just the stretching term. I can't understand why you would want bonds between all atoms within a certain distance, however, and I hope you know what you're doing. Erik 25 aug 2012 kl. 06.54 skrev mohan maruthi sena: Hi all, I want build a toplogy for a protein , for which , each and every atom has to make bonds with other atoms with in certain specified cut-off distance. How can i do this ? Please suggest me a way, 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 * 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
[gmx-users] Create a elastic network model -attach a spring between to atoms with force constant
Hi all, I want to create an elastic network model for a protein, in which i have selected only c-alpha atoms(removed rest of the atoms). To attach a spring between alpha atoms with some force(spring) constant k , How can i mention this in topology file ? 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] Tabulated potential 1-4 interactions
Hi all, I am using tabulated potential option for non bonded interactions. The system that i am using contains on CA(alpha) CB(beta) ,atoms connected, If i use option energygrps = CA CB energytable = CA CA CB CB it caluclates potential between CA CA and CB CB , CA CB. I also want to use tabulated potential for 1,4 atoms but this option does not take care of that, so how can i mention that option in mdp file so that it uses tabulated potential for 1,4 interaction also. Thanks in advance, Regards, 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
[gmx-users] unable to generate gro file -(only c alpha atoms -named as CB)
Hi all, My pdb file contains only c-alpha atoms , i have named alternate CA atoms(res) as CB(1res CA,2res CB,3res CA...) , I have given my residue name as ALB, accordingly i have changed .rtp ,atomtype files,residuetype.dat. i want to use force field(charmm27.ff) present in current directory using -ff option. These are the following errors that i am getting while trying to generate .gro ,.top files using pdb2gmx 1)using the following command i got , pdb2gmx -f 1ypi_ca_cb.pdb -o 1ypi.gro -p 1ypi.top -ff charmm27.ff error: Could not find force field 'charmm27.ff' in current directory, install tree or GMXDATA path. 2) when i used option export GMXLIB=/home/maruthi/1ypi to current directory error: atom N not found in buiding block 1ALB while combining tdb and rtp where as there are no N atom in my pdb file 3) when i used -ter option, and selected n-terminal none and c terminal none , i got the following error, WARNING: atom CB is missing in residue ALB 240 in the pdb file WARNING: atom CA is missing in residue ALB 241 in the pdb file WARNING: atom CB is missing in residue ALB 242 in the pdb file WARNING: atom CA is missing in residue ALB 243 in the pdb file WARNING: atom CB is missing in residue ALB 244 in the pdb file WARNING: atom CA is missing in residue ALB 245 in the pdb file WARNING: atom CB is missing in residue ALB 246 in the pdb file WARNING: atom CA is missing in residue ALB 247 in the pdb file WARNING: atom CB is missing in residue ALB 248 in the pdb file Fatal error: There were 247 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS I do not understand what went wrong , i hope the options i have used are correct. Please kindly suggest me a way to solve this. Thank you in advance, Regards, 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
[gmx-users] repulsive interaction i and i+2
Hi all, I have used a user define potential to describe attractive potential beyond i and i+3 atoms(similar to lLJ). If i want to describe repulsive interactions with in i and i+3 , how can i do it in gromacs? can anyone suggest me a way, Thanks and Regards, 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
[gmx-users] bonded interactions as table
Hi all, I have learned from manual that non bonded interactions can be given as user defined potential by using tables. If i want to give dihedral term as user defined potential keeping rest of the bonded parameters in their usual form, how can i do that. Please suggest me a way, Thanks Regards, 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
[gmx-users] user defined potential(repulsive) for atoms falling with in three residues
Hi all, I am using a user defined potential to describe non-bonded interactions, which describes attractive potential for residues separated by four or more bonds . Now I want to describe a user defined potential(repulsive) for atoms falling with in three residues and which are not determined to be attractive, as I tried to elaborate below: condition 1: if the two atoms are separated by four or more bonds i use attractive LJ potential. condition 2: if two atoms are not determined to be attractive or fall with in three bonds of each other(i, i+3) then their interaction is defined by repulsive term: E(rep)= epsilon (sigma/rij)^12 Please let me know how I can implement this in Gromacs. Thanks and Regards, 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
[gmx-users] How can i specify a user defined potential between i, i+2 residues
Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. T -- 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] Fwd: How can i specify a user defined potential between i, i+2 residues
Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. Thanks for a reply in advance, with regards, 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
[gmx-users] User defined potential
Hi all, I want to define a potential form and give it as input for which i have seen manual ,thought gromacs table option is fine, i have an example of generating 9-6 potential form , My question is how to generate table.xvg, what is the command to generate table.xvg from code table.c. with regards, 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
[gmx-users] Go model -error in generating topology
Hi all, I try to build go model(which uses only c-alpha atoms), my pdb contains only c-alpha atoms extracted from the original pdb file ,when i use pdb2gmx command on c-alpha containing pdb file it gives the following error. Atom N is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 1. Please suggest me a way , Thanking 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
[gmx-users] error in oscillation period
Hello everyone, I am getting the following error when i execute grompp command ,can anyone please explain me why this error arises, *NOTE 2 [file ile.top, line 2986]: The bond in molecule-type Protein_chain_I between atoms 22 N and 23 HN has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. *Thank you in advance, --Mohan gmx-users@gromacs.org -- 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
