[gmx-users] Normal Mode Analysis
Hi ALL, This may sound like a very basic question, but I am still pondering over it. I have simulated a membrane protein system for 30 ns after Steepest Descent minimization and now I want to perform NMA. From the help pages what I understand is that I need a very well minimized system (using l-bfgs) and then generate a Hessian matrix. My question is that after my 30 ns run, should I again go for another run of minimization with l-bfgs and the should I run MD using nm as the integrator? For how long should I run this MD with nm integrator? Is a 1 ns run enough? Or am I required to run it for 30 ns (for which I have run the normal MD)? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the trajectory I find unfolding of the original chain but the two additional peptide introduced through genconf show appearance of new secondary structures. Even in these two the secondary structure do not develop at the same point. Why the three equivalent peptide behave differently in similar environment. How can I explain this observation. why the first peptide does not show any new secondary structure. Sholud I go with higher number of molecule. Will it make any difference if peptides are added in disordered manner and then simulated. Shahid On 4/23/10, Mark Abraham mark.abra...@anu.edu.au wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf Well that's a difficult and atypical scenario. genconf -shuffle will allow you to stack the same peptide in a regular array with random rotations of the whole box. Then you can solvate, equilibrate and run MD at a high temperature to give yourself a quasi-disordered starting state. , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help me and write commands which I should follow. No, because that's an impossible task. We can't begin to guess the reasons for things failing without seeing the actual output (was the EM energy large and negative? what was the actual error message from -ci -nmol?). You should be careful to start with a small test case so that you can learn the workflow with a manageable problem. Can you get a single peptide to equilibrate? Two stacked peptides? It is best to learn to walk before trying to run :-) 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
shahid nayeem wrote: Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the trajectory I find unfolding of the original chain but the two additional peptide introduced through genconf show appearance of new secondary structures. Even in these two the secondary structure do not develop at the same point. Why the three equivalent peptide behave differently in similar environment. How can I explain this observation. why the first peptide does not show any new secondary structure. Sholud I go with higher number of molecule. Will it make any difference if peptides are added in disordered manner and then simulated. Initial orientation should likely have nothing to do with it. Perhaps this is even the proper behavior for whatever your peptide is. Is its structure dynamic? Is the size of your peptides large enough to even believe that they would be intrinsically stable? Many model peptides, in isolation, have very transient structures. It could also be that your simulation parameters are poorly chosen, so the force field is breaking down. If you want comments on your .mdp file, please post it. -Justin Shahid On 4/23/10, *Mark Abraham* mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf Well that's a difficult and atypical scenario. genconf -shuffle will allow you to stack the same peptide in a regular array with random rotations of the whole box. Then you can solvate, equilibrate and run MD at a high temperature to give yourself a quasi-disordered starting state. , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help me and write commands which I should follow. No, because that's an impossible task. We can't begin to guess the reasons for things failing without seeing the actual output (was the EM energy large and negative? what was the actual error message from -ci -nmol?). You should be careful to start with a small test case so that you can learn the workflow with a manageable problem. Can you get a single peptide to equilibrate? Two stacked peptides? It is best to learn to walk before trying to run :-) Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Normal Mode Analysis
Hi ALL, This may sound like a very basic question, but I am still pondering over it. I have simulated a membrane protein system for 30 ns after Steepest Descent minimization and now I want to perform NMA. From the help pages what I understand is that I need a very well minimized system (using l-bfgs) and then generate a Hessian matrix. My question is that after my 30 ns run, should I again go for another run of minimization with l-bfgs and the should I run MD using nm as the integrator? For how long should I run this MD with nm integrator? Is a 1 ns run enough? Or am I required to run it for 30 ns (for which I have run the normal MD)? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] help
hello i got the warning as the Warning: 1-4 interaction between 246 and 251 at distance 4.991 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Segmentation fault so tl me wt actually is table extension and table size in mdp file -- WITH REGARDS VANI -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] help
vani ms wrote: hello i got the warning as the Warning: 1-4 interaction between 246 and 251 at distance 4.991 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Segmentation fault so tl me wt actually is table extension and table size in mdp file Your system is blowing up. This is a well-documented event resulting from any number of factors, including insufficient minimization/equilibration, topology problems, incorrect .mdp file settings, and the like. For more: http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off http://www.gromacs.org/Documentation/Terminology/Blowing_Up If you want useful help, post a description of your system, how you built it, what you did to minimize and/or equilibrate, and what settings are in your .mdp file. Also please avoid abbreviating words for which there is no sensible reason. It makes reading emails difficult. -Justin -- WITH REGARDS VANI -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Normal Mode Analysis
Hi, NMA is not MD - for one thing you don't run an NMA simulation for a certain time. I suggest you read about NMA and make sure you understand what the method does and what it can achieve before continuing. There is some data on the manual, a lot of data on the web and even more in books. When you have a good idea on what is NMA and why you're interested in running it, you can try to run things and come back to the list with more specific questions if such arise. In parallel, it may be a good idea to read some papers where NMA was applied. I have in mind papers of Lindahl and Levitt from the recent years, but you should be able to come with an elaborate list. Good luck, Ran Anirban Ghosh wrote: Hi ALL, This may sound like a very basic question, but I am still pondering over it. I have simulated a membrane protein system for 30 ns after Steepest Descent minimization and now I want to perform NMA. From the help pages what I understand is that I need a very well minimized system (using l-bfgs) and then generate a Hessian matrix. My question is that after my 30 ns run, should I again go for another run of minimization with l-bfgs and the should I run MD using nm as the integrator? For how long should I run this MD with nm integrator? Is a 1 ns run enough? Or am I required to run it for 30 ns (for which I have run the normal MD)? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file Energy minimization cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.14 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = no Pcoupl = no gen_vel = no Position_restraint.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds constraintalgorithm = LINCS integrator = md dt = 0.002 ; ps ! nsteps = 25000 ; total 50 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.14 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Full_MD.mdp cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 500 ; total 1 ps. nstcomm = 1 nstxout = 5000 nstvout = 4 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.14 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 500 500 ; Energy monitoring energygrps = Protein Non-protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 500 K. gen_vel = no gen_temp = 500.0 gen_seed = 173529 shahid On 4/27/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the trajectory I find unfolding of the original chain but the two additional peptide introduced through genconf show appearance of new secondary structures. Even in these two the secondary structure do not develop at the same point. Why the three equivalent peptide behave differently in similar environment. How can I explain this observation. why the first peptide does not show any new secondary structure. Sholud I go with higher number of molecule. Will it make any difference if peptides are added in disordered manner and then simulated. Initial orientation should likely have nothing to do with it. Perhaps this is even the proper behavior for whatever your peptide is. Is its structure dynamic? Is the size of your peptides large enough to even believe that they would be intrinsically stable? Many model peptides, in isolation, have very transient structures. It could also be that your simulation parameters are poorly chosen, so the force field is breaking down. If you want comments on your .mdp file, please post it. -Justin Shahid On 4/23/10, *Mark Abraham* mark.abra...@anu.edu.au mailto: mark.abra...@anu.edu.au wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf Well that's a difficult and atypical scenario. genconf -shuffle will allow you to stack the same peptide in a regular array with random rotations of the whole box. Then you can solvate, equilibrate and run MD at a high temperature to give yourself a quasi-disordered starting state. , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help
Re: [gmx-users] more than one peptide in one simulation box
shahid nayeem wrote: My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file snip ref_t = 300 300 Here, you're equilibrating at 300 K... snip ref_t = 500 500 and here, you're running MD at 500 K, without any equilibration in between. That could be a problem, but more likely, the high temperature is simply causing the structure to break down. Short helices are usually not stable in isolation, and heating them to extreme conditions will probably accelerate this process. The various results you're seeing with different helices may just reflect that you haven't simulated long enough to see convergence in the structural features, but from what you've described, I expect what you're seeing is entirely normal, and almost predictable. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
On 27/04/2010 8:58 PM, Justin A. Lemkul wrote: shahid nayeem wrote: Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the trajectory I find unfolding of the original chain but the two additional peptide introduced through genconf show appearance of new secondary structures. Even in these two the secondary structure do not develop at the same point. Why the three equivalent peptide behave differently in similar environment. How can I explain this observation. why the first peptide does not show any new secondary structure. Sholud I go with higher number of molecule. Will it make any difference if peptides are added in disordered manner and then simulated. Initial orientation should likely have nothing to do with it. Perhaps this is even the proper behavior for whatever your peptide is. Is its structure dynamic? Is the size of your peptides large enough to even believe that they would be intrinsically stable? Many model peptides, in isolation, have very transient structures. It could also be that your simulation parameters are poorly chosen, so the force field is breaking down. If you want comments on your .mdp file, please post it. Indeed. MD is chaotic, and there's no reason to expect all peptides of any length to show the same actual behaviour in a trajectory. They might show the same behaviour in the limit of a converged ensemble, but only if aggregation is not a factor. Mark On 4/23/10, *Mark Abraham* mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf Well that's a difficult and atypical scenario. genconf -shuffle will allow you to stack the same peptide in a regular array with random rotations of the whole box. Then you can solvate, equilibrate and run MD at a high temperature to give yourself a quasi-disordered starting state. , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help me and write commands which I should follow. No, because that's an impossible task. We can't begin to guess the reasons for things failing without seeing the actual output (was the EM energy large and negative? what was the actual error message from -ci -nmol?). You should be careful to start with a small test case so that you can learn the workflow with a manageable problem. Can you get a single peptide to equilibrate? Two stacked peptides? It is best to learn to walk before trying to run :-) Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mutation to/from proline
On 25/04/2010 10:18 PM, afsaneh maleki wrote: Hi, I want to calculate relative free energy associated to mutation of P1 (native protein) to p2 (mutated protein).In this mutation, Isolusine (in P1) is mutated to Proline(in P2). With using Thermodynamic cycle: Bilayer+P1= = = Bilayer-P1 delta G1 (association P1) Bilayer+P2= = = Bilayer-P2 delta G2 (association P2) Where P1 = = = P2 deltaG3 Bilayer-P1 = = = Bilayer-P2 deltaG4 So, delta deltaG= (delta G1(association P1)- deltaG2 (association P2))= (deltaG3- deltaG4) To define the B state that will be used for the free energy calculation. For this; I need to specify the new atom type of each mutated atom and the set of parameters to it. But my question is that with regarding to special structure of proline, is it possible to update topology file? Who was done mutation of proline before? I searched but I didn’t find! Or is there manual for mutating from/to proline? That's a pretty significant perturbation to be trying to study, because there have to be protein backbone rearrangements to accommodate proline, mutation of methyl to H, and a free alkyl chain losing its entropy and a pair of H. I expect you'll need to do a phenomenal amount of sampling to get useful results, even if you can think of a sensible mutation reaction coordinate. It would not surprise me if such a mutation had not been reported in the literature. Accordingly, you might be best served by such methods implemented for implicit solvation in some other simulation package (if such exists). 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] Skickat: den 27 april 2010 12:41 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.orgmailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Interfacial systems such as membranes can translate independently of surrounding aqueous solvent. Thus, the lipids could move one way, the water can move in the other way, but overall, the net COM motion is zero. If you specify two groups, as Xavier suggested, you treat the COM motion more appropriately. So, more specifically: comm-grps = DPPC_CHOL_MOL SOL ...replacing, of course, whatever your small molecule name where I have MOL. You will need a custom index group created by make_ndx to generate this first group. -Justin Sorry that I didn't understand you explanation. Emma *Från:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] *Skickat:* den 27 april 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface
Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box
you should remove the water and lipid bilayer COM separately. I am not sure what you should do with your small molecule though. Probably best to add it to the bilayer as you constrain their relative position! On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: Hi again, Thanks Xavier for your reply. I didn't know that this mdp option existed. However, I read the manual and also checked the mdout.mdp files for my previous simulations, and I understood it as if those are the default settings even if you don't specify any of them in the md.mdp file. The default comm_groups is the whole system so I guess if I'm not writing anything there it will take the whole system. In that case I think that in my previous simulations the translational motion should have been removed for the whole system, but since it's obviously not remove something is wrong. Or did I misunderstand everything? My system consists of DPPC lipids, cholesterol, water and one small molecule. Should I specify comm_groups as only the lipids? In that case I get a warning from grompp. You wrote comm-grps = membrane solvent + ions. Only the water then? Sorry that I didn't understand you explanation. Emma Från: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] för XAvier Periole [x.peri...@rug.nl] Skickat: den 27 april 2010 12:41 Till: Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box The crash seems to be expected as by crossing the pbc the distance will change significantly and in way the algorithm can not handle. Note that the overall translational motion of your system should always be removed. The removal of the COM motion of your bilayer should be sufficient to prevent the overall motion of the bilayer. have a look at the following option in the mdp: ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= membrane solvent+ions On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: Hi all! I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks. Emma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] help
hello. I got the same error, because I was using an NPT ensemble to do a position-restrained simulation, and the error disappeared when I did the position-restrained simulation with NVT. Best regards. Lucio. El mar, 27-04-2010 a las 16:52 +0530, vani ms escribió: hello i got the warning as the Warning: 1-4 interaction between 246 and 251 at distance 4.991 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Segmentation fault so tl me wt actually is table extension and table size in mdp file -- WITH REGARDS VANI -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] help
Lucio Ricardo Montero Valenzuela wrote: hello. I got the same error, because I was using an NPT ensemble to do a position-restrained simulation, and the error disappeared when I did the position-restrained simulation with NVT. I would be careful about ad hoc changes to the statistical mechanical ensemble to try to circumvent a problem like this one. The answer to these types of errors is always the same: the model physics has broken, causing the system to explode. There are several reasons for this to occur, and in your case, perhaps your system simply wasn't ready for pressure coupling :) The original poster has provided insufficient information about the system to provide anything beyond speculation as to how to fix this problem. -Justin Best regards. Lucio. El mar, 27-04-2010 a las 16:52 +0530, vani ms escribió: hello i got the warning as the Warning: 1-4 interaction between 246 and 251 at distance 4.991 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Segmentation fault so tl me wt actually is table extension and table size in mdp file -- WITH REGARDS VANI -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Ensemble averaging between two proteins in the same box.
Hi, all, I am trying to do distance restraints under two different conditions of the protein. I have both of these proteins in the same box. Because the experimentally determined distance restraints are from the same signal, there are distance restraints between similar atoms in both structures. In other words, they have the same index. However, Gromacs says that it does not have this capability, yet. Is there a work around? Thank you in advance. Much appreciated, Art Art Roberts 3950 Mahaila Ave G18 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com skype=aroberts92122 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Solvent addition
tekle...@ualberta.ca wrote: Dear Gromacs users, I have a box 10 X 10 X 10 with 20 solute molecules in side it. I want to add a solvent of 25% X and 75% Y and so on to see the aggregation behavior of my molecules in different ratio of solvents X and Y. Can any body help me how to do this. The two solvent is mixed. e.g 25% X and 75% Y = desired Solvent http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin Rob -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Solvent addition
Dear Gromacs users, I have a box 10 X 10 X 10 with 20 solute molecules in side it. I want to add a solvent of 25% X and 75% Y and so on to see the aggregation behavior of my molecules in different ratio of solvents X and Y. Can any body help me how to do this. The two solvent is mixed. e.g 25% X and 75% Y = desired Solvent Rob -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] I noticed implicit_solvent in the mdout.mdp. Is it going to be implemented soon?
Hi, all, I noticed that there was an implicit_solvent term in the mdout.mdp. However, it didn't seem operative. I am just curious. Is it going to be implemented soon? Sincerely, Art Art Roberts 3950 Mahaila Ave G18 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com skype=aroberts92122 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] h_bond error
Hi, I'm trying to compute H bonds in a protein-ligand system. I got the following error: Program g_hbond, VERSION 4.0.7 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. I use the line *g_hbond -f file.xtc -s file.tpr -n index.ndx -g HBOND_log -num HBOND* *file.xtc = THis is my file with concatenate trajectories.* I didnt find anywhere about this error. Someone know how to fix it? Thanks! -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] h_bond error
Maurício Menegatti Rigo wrote: Hi, I'm trying to compute H bonds in a protein-ligand system. I got the following error: Program g_hbond, VERSION 4.0.7 Source code file: gmx_hbond.c, line: 565 Fatal error: Error in func_type Position Rest. I use the line *g_hbond -f file.xtc -s file.tpr -n index.ndx -g HBOND_log -num HBOND* /file.xtc = THis is my file with concatenate trajectories./ I didnt find anywhere about this error. Someone know how to fix it? Interesting, I answered an identical post exactly one week ago: http://lists.gromacs.org/pipermail/gmx-users/2010-April/050254.html There is a work-around in that thread. -Justin Thanks! -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] h_bond error
Thanks J. My mistake. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RDF
Hello, I am trying to plot radial distribution function between a atom and a center of two atoms. How can I calculate the centre of two atoms and further how can I use this center to plot radial distribution funciton? THanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how many dihedral angles should be included for the naphthalene molecule if I use oplsaa
Dear all, I want to test a MD simulation job for the naphthalene molecule by the oplsaa force field by. The x2top generated less number of dihedral angles than what I expected. Do you know how many dihedral angles should be included for the naphthalene molecule if I use oplsaa? Thanks a lot. Ming -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how many dihedral angles should be included for the naphthalene molecule if I use oplsaa
Ming Han wrote: Dear all, I want to test a MD simulation job for the naphthalene molecule by the oplsaa force field by. The x2top generated less number of dihedral angles than what I expected. Do you know how many dihedral angles should be included for the naphthalene molecule if I use oplsaa? It would be helpful to see the [dihedrals] directive that x2top produced, as well as an explanation of what you think you should've gotten. Just saying you got less than what you thought isn't very informative. You may also want to consult the primary literature for OPLS to see the derivation of bonded parameters and how they might be applied to naphthalene. -Justin Thanks a lot. Ming -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how many dihedral angles should be included for the naphthalene molecule if I use oplsaa
1__2 6__ // 3\/ \\ |||4| \\___ /\___// 5 7 I want to know if 1-2-3-6 torsion should be included? And if both 2-3-4-7 and 6-3-4-5 should be included? Thanks. Ming On Tue, Apr 27, 2010 at 6:43 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ming Han wrote: Dear all, I want to test a MD simulation job for the naphthalene molecule by the oplsaa force field by. The x2top generated less number of dihedral angles than what I expected. Do you know how many dihedral angles should be included for the naphthalene molecule if I use oplsaa? It would be helpful to see the [dihedrals] directive that x2top produced, as well as an explanation of what you think you should've gotten. Just saying you got less than what you thought isn't very informative. You may also want to consult the primary literature for OPLS to see the derivation of bonded parameters and how they might be applied to naphthalene. -Justin Thanks a lot. Ming -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how many dihedral angles should be included for the naphthalene molecule if I use oplsaa
Ming Han wrote: 1__2 6__ // 3\/ \\ |||4| \\___ /\___// 5 7 I want to know if 1-2-3-6 torsion should be included? And if both 2-3-4-7 and 6-3-4-5 should be included? Thanks. I would think that proper dihedrals would not even be used for such a molecule. The fused ring systems will utilize impropers to stay planar. For example, the TRP side chain specifies no proper dihedrals within the indole side chain; only impropers are used, but maybe someone with more OPLS derivation experience can comment. You can also look into the literature. A simple Google search for napthalene OPLS (without the quotes) turns up tons of simulation papers. -Justin Ming On Tue, Apr 27, 2010 at 6:43 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ming Han wrote: Dear all, I want to test a MD simulation job for the naphthalene molecule by the oplsaa force field by. The x2top generated less number of dihedral angles than what I expected. Do you know how many dihedral angles should be included for the naphthalene molecule if I use oplsaa? It would be helpful to see the [dihedrals] directive that x2top produced, as well as an explanation of what you think you should've gotten. Just saying you got less than what you thought isn't very informative. You may also want to consult the primary literature for OPLS to see the derivation of bonded parameters and how they might be applied to naphthalene. -Justin Thanks a lot. Ming -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
Hi Justin Should I try to do position restraint at 500k and then full MD simulation. shahid On 4/27/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: My peptide is 26 residue alpha helix obtained from crystal structure .pdb file. I am posting energy minimization, position restarint and full MD simulation .mdp file snip ref_t = 300 300 Here, you're equilibrating at 300 K... snip ref_t = 500 500 and here, you're running MD at 500 K, without any equilibration in between. That could be a problem, but more likely, the high temperature is simply causing the structure to break down. Short helices are usually not stable in isolation, and heating them to extreme conditions will probably accelerate this process. The various results you're seeing with different helices may just reflect that you haven't simulated long enough to see convergence in the structural features, but from what you've described, I expect what you're seeing is entirely normal, and almost predictable. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
Hi Mark How one should be certain that this much trajectory is long enough to get coverged ensemble. Shahid On 4/27/10, Mark Abraham mark.abra...@anu.edu.au wrote: On 27/04/2010 8:58 PM, Justin A. Lemkul wrote: shahid nayeem wrote: Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the trajectory I find unfolding of the original chain but the two additional peptide introduced through genconf show appearance of new secondary structures. Even in these two the secondary structure do not develop at the same point. Why the three equivalent peptide behave differently in similar environment. How can I explain this observation. why the first peptide does not show any new secondary structure. Sholud I go with higher number of molecule. Will it make any difference if peptides are added in disordered manner and then simulated. Initial orientation should likely have nothing to do with it. Perhaps this is even the proper behavior for whatever your peptide is. Is its structure dynamic? Is the size of your peptides large enough to even believe that they would be intrinsically stable? Many model peptides, in isolation, have very transient structures. It could also be that your simulation parameters are poorly chosen, so the force field is breaking down. If you want comments on your .mdp file, please post it. Indeed. MD is chaotic, and there's no reason to expect all peptides of any length to show the same actual behaviour in a trajectory. They might show the same behaviour in the limit of a converged ensemble, but only if aggregation is not a factor. Mark On 4/23/10, *Mark Abraham* mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf Well that's a difficult and atypical scenario. genconf -shuffle will allow you to stack the same peptide in a regular array with random rotations of the whole box. Then you can solvate, equilibrate and run MD at a high temperature to give yourself a quasi-disordered starting state. , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help me and write commands which I should follow. No, because that's an impossible task. We can't begin to guess the reasons for things failing without seeing the actual output (was the EM energy large and negative? what was the actual error message from -ci -nmol?). You should be careful to start with a small test case so that you can learn the workflow with a manageable problem. Can you get a single peptide to equilibrate? Two stacked peptides? It is best to learn to walk before trying to run :-) Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] more than one peptide in one simulation box
On 28/04/10 15:13, shahid nayeem wrote: Hi Mark How one should be certain that this much trajectory is long enough to get coverged ensemble. When the observables of interest aren't changing... This is a how long is a piece of string?-type question. Read some literature about simulations of similar systems. Think many hundreds of nanoseconds, probably. Mark On 4/27/10, *Mark Abraham* mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 27/04/2010 8:58 PM, Justin A. Lemkul wrote: shahid nayeem wrote: Dear Mark Following your advice I started using three peptide in one simulation box. Iwas able to add these with genconf as previously in ordered manner, generated .gro with genconf, solvated it and after energy minimization I did MD run for 10ns. Everything ran well. In the end when I see the trajectory I find unfolding of the original chain but the two additional peptide introduced through genconf show appearance of new secondary structures. Even in these two the secondary structure do not develop at the same point. Why the three equivalent peptide behave differently in similar environment. How can I explain this observation. why the first peptide does not show any new secondary structure. Sholud I go with higher number of molecule. Will it make any difference if peptides are added in disordered manner and then simulated. Initial orientation should likely have nothing to do with it. Perhaps this is even the proper behavior for whatever your peptide is. Is its structure dynamic? Is the size of your peptides large enough to even believe that they would be intrinsically stable? Many model peptides, in isolation, have very transient structures. It could also be that your simulation parameters are poorly chosen, so the force field is breaking down. If you want comments on your .mdp file, please post it. Indeed. MD is chaotic, and there's no reason to expect all peptides of any length to show the same actual behaviour in a trajectory. They might show the same behaviour in the limit of a converged ensemble, but only if aggregation is not a factor. Mark On 4/23/10, *Mark Abraham* mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/04/10 13:16, shahid nayeem wrote: Dear All I am trying to study inter peptide interaction fpr which I need to put more than one peptide in one simulation box. I did it with genconf command but this inserts peptide in a regular ordered manner I want these to be in irregular disordered insertion. Even after using genconf Well that's a difficult and atypical scenario. genconf -shuffle will allow you to stack the same peptide in a regular array with random rotations of the whole box. Then you can solvate, equilibrate and run MD at a high temperature to give yourself a quasi-disordered starting state. , I tried to proceed furthe after solvation with spc water. The energy minimization (steepest descent) failed to converge even after 5000 steps and theirafter position restraint dynamics failed giving segmentation fault. Introducing more peptide after generating .gro with -ci -nmol gives error showing more than one residue in insert molecule. Please help me and write commands which I should follow. No, because that's an impossible task. We can't begin to guess the reasons for things failing without seeing the actual output (was the EM energy large and negative? what was the actual error message from -ci -nmol?). You should be careful to start with a small test case so that you can learn the workflow with a manageable problem. Can you get a single peptide to equilibrate? Two stacked peptides? It is best to learn to walk before trying to run :-) Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive
Re: [gmx-users] Freezing a portion of a protein during simulation
Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include water topology #include spc.itp - And in my .mdp file I am giving: - define = -DSTRONG_POSRES ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs --- But now what I am getting is that if I run MD using these restraints on the helical portion of the protein, then I am getting LINCS errors. However, if I allow the entire protein to move during MD, then it is running fine. What mistake am I making? And how can I freeze properly the helical portions and simulate only the loop? Thanks a lot in advance. Regards, Anirban On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I want to do a MD simulation by restraining (freezing) the helical portions and allowing only the loop regions to move. I tried doing this by applying heavy restrain on the helical residues by generating a .itp file with the genrestr command with an index file containing the desired residue numbers. However during the simulation I am finding that the entire protein is moving. Am I doing anything wrong? Or is there any other way to freeze a portion of a protein? Any suggestion is welcome. thanks a lot in advance. If your protein is still moving, then you aren't correctly applying your position restraints. Without seeing your topology and .mdp file, there's no way to know what you're doing wrong. You can also use the freezegrps option in the .mdp file, but then you also have to make sure you're using the appropriate energygrp_excl, etc. It is generally much easier to apply position restraints. -Justin Regards, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
