[gmx-users] Re: Is there a way to omit particles with q=0, from Coulomb-/PME-calculations?
On 17/01/2012 4:55 AM, Thomas Schlesier wrote: Dear all, Is there a way to omit particles with zero charge from calculations for Coulomb-interactions or PME? In my calculations i want to coarse-grain my solvent, but the solute should be still represented by atoms. In doing so the solvent-molecules have a zero charge. I noticed that for a simulation with only the CG-solvent significant time was spent for the PME-part of the simulation. If i would simulate the complete system (atomic solute + coarse-grained solvent), i would save only time for the reduced number of particles (compared to atomistic solvent). But if i could omit the zero-charge solvent from the Coulomb-/PME-part, it would save much additional time. Is there an easy way for the omission, or would one have to hack the code? If the latter is true, how hard would it be and where do i have to look? (First idea would be to create an index-file group with all non-zero-charged particles and then run in the loops needed for Coulomb/PME only over this subset of particles.) I have only experience with Fortran and not with C++. Only other solution which comes to my mind would be to use plain cut-offs for the Coulomb-part. This would save time required for doing PME but will in turn cost time for the calculations of zeros (Coulomb-interaction for the CG-solvent). But more importantly would introduce artifacts from the plain cut-off :( Particles with zero charge are not included in neighbour lists used for calculating Coulomb interactions. The statistics in the M E G A - F L O P S A C C O U N T I N G section of the .log file will show that there is significant use of loops that do not have Coul component. So already these have no effect on half of the PME calculation. I don't know whether the grid part is similarly optimized, but you can test this yourself by comparing timing of runs with and without charged solvent. Mark Ok, i will test this. But here is the data i obtained for two simulations, one with plain cut-off and the other with PME. As one sees the simulation with plain cut-offs is much faster (by a factor of 6). --- With PME: M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops --- VdW(T) 1132.029152 61129.574 0.1 Outer nonbonded loop1020.997718 10209.977 0.0 Calc Weights 16725.001338 602100.048 0.6 Spread Q Bspline 356800.028544 713600.057 0.7 Gather F Bspline 356800.028544 4281600.343 4.4 3D-FFT 9936400.79491279491206.35981.6 Solve PME 18.0144001152.92211.8 NS-Pairs2210.718786 46425.095 0.0 Reset In Box1115.003345.000 0.0 CG-CoM 1115.0004463345.001 0.0 Virial 7825.000626 140850.011 0.1 Ext.ens. Update 5575.000446 301050.024 0.3 Stop-CM 5575.000446 55750.004 0.1 Calc-Ekin 5575.000892 150525.024 0.2 --- Total 97381137.440 100.0 --- D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 94.1 Average load imbalance: 10.7 % Part of the total run time spent waiting due to load imbalance: 0.1 % R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 4250 903.835 308.1 1.8 Comm. coord. 4 1251 321.930 109.7 0.6 Neighbor search4251 1955.330 666.5 3.8 Force 4 1251 696.668 237.5 1.4 Wait + Comm. F 4 1251 384.107 130.9 0.7 PME mesh 4 125143854.81814948.285.3 Write traj.4 50011.4890.5 0.0 Update 4 1251 1137.630 387.8 2.2 Comm. energies 4 1251 1074.541 366.3 2.1 Rest 41093.194 372.6 2.1 --- Total
[gmx-users] micelle formation
Dear Specialists, I am a beginner in grmacs and I have several questions about formation of micelle in gromacs. Please help me. 1- We know that there is a thermodynamic equilibrium between created micelle and free monomers in solvent, but I don't see this in results of my simulation! When I add the number of monomers, all of them are aggregated depend of concentration of solution in one micelle (spherical to cylindrical) or several micelles and always, lack of single monomer is the most stable state for system. also, I didn't find this in previous work by gromacs. Is it the limitation of gramacs? Why? 2- What is the relation of radius of gyration with effective radius of spherical micelle that in many of papers have been pointed to R(micelle)=(1.291)R(gyration)? 3- Where is the center of mass of micelle in gromacs, exactly? I obtained rdf for tails of surfactants with center of mass of micelle that the first part of file is as following:( I work with martini and we know that sigma= 0.47 nm in L-J) 0 0 0.002 0 0.004 0 0.006 0 0.008 0 0.01 0 0.012 0 0.014 0 0.016 0 0.018 0 0.02 0 0.022 0 0.024 0 0.026 0 0.028 0 0.03 0 0.032 0 0.034 91.8328 0.036 0 0.038 0 0.04 0 0.042 60.1866 0.044 0 0.046 50.176 0.048 46.0824 0.05 42.4701 0.052 39.2663 0.054 0 0.056 33.8578 0.058 0 0.06 29.4943 0.062 27.6223 0.064 0 0.066 48.7518 0.068 0 0.07 21.6699 0.072 0 0.074 19.3906 0.076 0 0.078 0 0.08 82.9561 0.082 47.3753 0.084 0 0.086 0 0.088 0 0.09 39.3277 0.092 0 0.094 12.0173 0.096 23.0438 0.098 11.0564 0.1 0 0.102 20.4125 0.104 19.635 0.106 9.45052 0.108 9.10376 0.11 17.5514 0.112 0 0.114 0 0.116 7.89139 ... ... What does it mean? Does it say me that the center of micelle is where the end of tails reach together. Do the tails bond in the center of micelle together or there is a hole according to my result and what is your definition in gromacs for center of mass of micelle, hole or bond between tails, Please? I took rdf for last bead of tails together that the first part of file is as: 0 0 0.002 0 0.004 0 0.006 0 0.008 0 ..0 ..0 ..0 0.414 0 0.416 0 0.418 0 0.42 0 0.422 0 0.424 0 0.426 0.0577916 0.428 0 0.43 0.113443 and maximum g(r) is in 0.512 nm (the first peak) and in distance 0.47 nm, g(r) is 50.3262. Can I interpret that tails are in two states together: bonded and non-bonded but maximum of tails are non-bonded, therefore, there is a hole in the center of micelle? Please help me. Thank you very much in advance. Best Regards Dina-- 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] Question about nsttcouple
On 17/01/2012 7:53 PM, Size Zheng wrote: Dear All, We are doing a simulation for ice melting in Efield with thermostat, and we would like to control the frequency for coupling the temperature by setting nsttcouple. But we always received a warning said it was a unknown parameter during grompp in GROMACS V4.0.7 on LINUX. I also tried it by GROMACS V4.5.4 on my MAC OS, it was done successfully. Unfortunately, our HPC uses GROMACS V4.0.7, so it is a problem for us. Functionality changes from version to version, and you are observing that here. Is there anything we did incorrectly? Any suggestions? Install a more recent version. It's (much) less than an hour's work for an experienced sysadmin, and runs faster as well. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] micelle formation
On 17/01/2012 7:37 PM, dina dusti wrote: Dear Specialists, I am a beginner in grmacs and I have several questions about formation of micelle in gromacs. Please help me. 1- We know that there is a thermodynamic equilibrium between created micelle and free monomers in solvent, but I don't see this in results of my simulation! When I add the number of monomers, all of them are aggregated depend of concentration of solution in one micelle (spherical to cylindrical) or several micelles and always, lack of single monomer is the most stable state for system. also, I didn't find this in previous work by gromacs. Is it the limitation of gramacs? Why? It has nothing to do with GROMACS, and likely everything to do with your choice of model physics and the degree of convergence of the simulation. 2- What is the relation of radius of gyration with effective radius of spherical micelle that in many of papers have been pointed to R(micelle)=(1.291)R(gyration)? I don't understand your question, or how it relates to GROMACS :) 3- Where is the center of mass of micelle in gromacs, exactly? I obtained rdf for tails of surfactants with center of mass of micelle that the first part of file is as following:( I work with martini and we know that sigma= 0.47 nm in L-J) 00 0.002 0 0.004 0 0.006 0 0.008 0 0.01 0 0.012 0 0.014 0 0.016 0 0.018 0 0.02 0 0.022 0 0.024 0 0.026 0 0.028 0 0.03 0 0.032 0 0.03491.8328 0.036 0 0.038 0 0.04 0 0.04260.1866 0.044 0 0.046 50.176 0.04846.0824 0.0542.4701 0.05239.2663 0.054 0 0.05633.8578 0.058 0 0.0629.4943 0.06227.6223 0.064 0 0.06648.7518 0.068 0 0.0721.6699 0.072 0 0.07419.3906 0.076 0 0.078 0 0.0882.9561 0.08247.3753 0.084 0 0.086 0 0.088 0 0.0939.3277 0.092 0 0.09412.0173 0.09623.0438 0.09811.0564 0.1 0 0.10220.4125 0.104 19.635 0.1069.45052 0.1089.10376 0.1117.5514 0.112 0 0.114 0 0.1167.89139 ... ... What does it mean? Does it say me that the center of micelle is where the end of tails reach together. Do the tails bond in the center of micelle together or there is a hole according to my result and what is your definition in gromacs for center of mass of micelle, hole or bond between tails, Please? We don't even know whether your micelles should have monomer tails in the center or outside, or how you generated those numbers or what they are. If that's a radial distribution function, then you probably want to choose a narrower bin width for computing it, and get a lot more samples to go in it. I took rdf for last bead of tails together that the first part of file is as: 0 0 0.002 0 0.004 0 0.006 0 0.008 0 ..0 ..0 ..0 0.414 0 0.416 0 0.418 0 0.42 0 0.422 0 0.424 0 0.426 0.0577916 0.428 0 0.43 0.113443 and maximum g(r) is in 0.512 nm (the first peak) and in distance 0.47 nm, g(r) is 50.3262. Can I interpret that tails are in two states together: bonded and non-bonded but maximum of tails are non-bonded, therefore, there is a hole in the center of micelle? I don't know, but some well-chosen use of g_rdf or g_density might get the information you seek if it's there to be found. Make sure you visualize the simulation first. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Is there a way to omit particles with, q=0, from Coulomb-/PME-calculations?
But would there be a way to optimize it further? In my real simulation i would have a charged solute and the uncharged solvent (both have nearly the same number of particles). If i could omit the uncharged solvent from the long-ranged coulomb-calculation (PME) it would save much time. Or is there a reason that some of the PME stuff is also calculated for uncharged particles? (Ok, i know that this is a rather specical system, in so far that in most md-simulations the number of uncharged particles is negligible.) Would it be probably better to move the question to the developer-list? Greetings Thomas On 17/01/2012 7:32 PM, Thomas Schlesier wrote: On 17/01/2012 4:55 AM, Thomas Schlesier wrote: Dear all, Is there a way to omit particles with zero charge from calculations for Coulomb-interactions or PME? In my calculations i want to coarse-grain my solvent, but the solute should be still represented by atoms. In doing so the solvent-molecules have a zero charge. I noticed that for a simulation with only the CG-solvent significant time was spent for the PME-part of the simulation. If i would simulate the complete system (atomic solute + coarse-grained solvent), i would save only time for the reduced number of particles (compared to atomistic solvent). But if i could omit the zero-charge solvent from the Coulomb-/PME-part, it would save much additional time. Is there an easy way for the omission, or would one have to hack the code? If the latter is true, how hard would it be and where do i have to look? (First idea would be to create an index-file group with all non-zero-charged particles and then run in the loops needed for Coulomb/PME only over this subset of particles.) I have only experience with Fortran and not with C++. Only other solution which comes to my mind would be to use plain cut-offs for the Coulomb-part. This would save time required for doing PME but will in turn cost time for the calculations of zeros (Coulomb-interaction for the CG-solvent). But more importantly would introduce artifacts from the plain cut-off :( Particles with zero charge are not included in neighbour lists used for calculating Coulomb interactions. The statistics in the M E G A -F L O P S A C C O U N T I N G section of the .log file will show that there is significant use of loops that do not have Coul component. So already these have no effect on half of the PME calculation. I don't know whether the grid part is similarly optimized, but you can test this yourself by comparing timing of runs with and without charged solvent. Mark Ok, i will test this. But here is the data i obtained for two simulations, one with plain cut-off and the other with PME. As one sees the simulation with plain cut-offs is much faster (by a factor of 6). Yes. I think I have seen this before for PME when (some grid cells) are lacking (many) charged particles. You will see that the nonbonded loops are always VdW(T) for tabulated VdW - you have no charges at all in this system and GROMACS has already optimized its choice of nonbonded loops accordingly. You would see Coul(T) + VdW(T) if your solvent had charge. It's not a meaningful test of the performance of PME vs cut-off, either, because there are no charges. Mark --- With PME: M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops --- VdW(T) 1132.029152 61129.574 0.1 Outer nonbonded loop1020.997718 10209.977 0.0 Calc Weights 16725.001338 602100.048 0.6 Spread Q Bspline 356800.028544 713600.057 0.7 Gather F Bspline 356800.028544 4281600.343 4.4 3D-FFT 9936400.79491279491206.35981.6 Solve PME 18.0144001152.92211.8 NS-Pairs2210.718786 46425.095 0.0 Reset In Box1115.003345.000 0.0 CG-CoM 1115.0004463345.001 0.0 Virial 7825.000626 140850.011 0.1 Ext.ens. Update 5575.000446 301050.024 0.3 Stop-CM 5575.000446 55750.004 0.1 Calc-Ekin 5575.000892 150525.024 0.2 --- Total 97381137.440 100.0 --- D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step
[gmx-users] micelle formation
Dear Prof. Thank you very much from your reply. My question about R(micelle)=(1.291)R(gyration) is that, what is cause of coefficient 1.29? Yes, I saw one micelle that the tails of surfactants are into the micelle and heads are out of micelle visually (consist of 80 monomer). My results that I sent you are the results of g_rdf for tail with the center of mass of micelle and g_rdf for the last bead of tail to its own (for both of them I did g_rdf with options -b 10 -e 30, means time from micelle formation to end) and I sent you just the first part of file and that file is for 30 ps originally. My problem is about interpret for the first part of file that is representative of hole in the center of micelle or no, and is it our expectancy in gromacs? My question about the center of mass of micelle is because of I want to know that is there the way for computation of radius of hole of the center of micelle? Thank you very much again. Best Regards Dina -- 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] Is there a way to omit particles with, q=0, from Coulomb-/PME-calculations?
Hi Thomas, Am Jan 17, 2012 um 10:29 AM schrieb Thomas Schlesier: But would there be a way to optimize it further? In my real simulation i would have a charged solute and the uncharged solvent (both have nearly the same number of particles). If i could omit the uncharged solvent from the long-ranged coulomb-calculation (PME) it would save much time. Or is there a reason that some of the PME stuff is also calculated for uncharged particles? For PME you need the Fourier-transformed charge grid and you get back the potential grid from which you interpolate the forces on the charged atoms. The charges are spread each on typically 4x4x4 (=PME order) grid points, and in this spreading only charged atoms will take part. So the spreading part (and also the force interpolation part) will become faster with less charges. However, the rest of PME (the Fourier transforms and calculations in reciprocal space) are unaffected by the number of charges. For this only the size of the whole PME grid matters. You could try to lower the number of PME grid points (enlarge fourierspacing) and at the same time enhance the PME order (to 6 for example) to keep a comparable force accuracy. You could also try to shift more load to real space, which will also lower the number of PME grid points (g_tune_pme can do that for you). But I am not shure that you can get large performance benefits from that. Best, Carsten (Ok, i know that this is a rather specical system, in so far that in most md-simulations the number of uncharged particles is negligible.) Would it be probably better to move the question to the developer-list? Greetings Thomas On 17/01/2012 7:32 PM, Thomas Schlesier wrote: On 17/01/2012 4:55 AM, Thomas Schlesier wrote: Dear all, Is there a way to omit particles with zero charge from calculations for Coulomb-interactions or PME? In my calculations i want to coarse-grain my solvent, but the solute should be still represented by atoms. In doing so the solvent-molecules have a zero charge. I noticed that for a simulation with only the CG-solvent significant time was spent for the PME-part of the simulation. If i would simulate the complete system (atomic solute + coarse-grained solvent), i would save only time for the reduced number of particles (compared to atomistic solvent). But if i could omit the zero-charge solvent from the Coulomb-/PME-part, it would save much additional time. Is there an easy way for the omission, or would one have to hack the code? If the latter is true, how hard would it be and where do i have to look? (First idea would be to create an index-file group with all non-zero-charged particles and then run in the loops needed for Coulomb/PME only over this subset of particles.) I have only experience with Fortran and not with C++. Only other solution which comes to my mind would be to use plain cut-offs for the Coulomb-part. This would save time required for doing PME but will in turn cost time for the calculations of zeros (Coulomb-interaction for the CG-solvent). But more importantly would introduce artifacts from the plain cut-off :( Particles with zero charge are not included in neighbour lists used for calculating Coulomb interactions. The statistics in the M E G A -F L O P S A C C O U N T I N G section of the .log file will show that there is significant use of loops that do not have Coul component. So already these have no effect on half of the PME calculation. I don't know whether the grid part is similarly optimized, but you can test this yourself by comparing timing of runs with and without charged solvent. Mark Ok, i will test this. But here is the data i obtained for two simulations, one with plain cut-off and the other with PME. As one sees the simulation with plain cut-offs is much faster (by a factor of 6). Yes. I think I have seen this before for PME when (some grid cells) are lacking (many) charged particles. You will see that the nonbonded loops are always VdW(T) for tabulated VdW - you have no charges at all in this system and GROMACS has already optimized its choice of nonbonded loops accordingly. You would see Coul(T) + VdW(T) if your solvent had charge. It's not a meaningful test of the performance of PME vs cut-off, either, because there are no charges. Mark --- With PME: M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops --- VdW(T) 1132.029152 61129.574 0.1 Outer nonbonded loop1020.997718 10209.977 0.0 Calc Weights
[gmx-users] Re: Is there a way to omit particles with, q=0, from, Coulomb-/PME-calculations?
Thanks Carsten. Now i see the problem. Hi Thomas, Am Jan 17, 2012 um 10:29 AM schrieb Thomas Schlesier: But would there be a way to optimize it further? In my real simulation i would have a charged solute and the uncharged solvent (both have nearly the same number of particles). If i could omit the uncharged solvent from the long-ranged coulomb-calculation (PME) it would save much time. Or is there a reason that some of the PME stuff is also calculated for uncharged particles? For PME you need the Fourier-transformed charge grid and you get back the potential grid from which you interpolate the forces on the charged atoms. The charges are spread each on typically 4x4x4 (=PME order) grid points, and in this spreading only charged atoms will take part. So the spreading part (and also the force interpolation part) will become faster with less charges. However, the rest of PME (the Fourier transforms and calculations in reciprocal space) are unaffected by the number of charges. For this only the size of the whole PME grid matters. You could try to lower the number of PME grid points (enlarge fourierspacing) and at the same time enhance the PME order (to 6 for example) to keep a comparable force accuracy. You could also try to shift more load to real space, which will also lower the number of PME grid points (g_tune_pme can do that for you). But I am not shure that you can get large performance benefits from that. Best, Carsten (Ok, i know that this is a rather specical system, in so far that in most md-simulations the number of uncharged particles is negligible.) Would it be probably better to move the question to the developer-list? Greetings Thomas On 17/01/2012 7:32 PM, Thomas Schlesier wrote: On 17/01/2012 4:55 AM, Thomas Schlesier wrote: Dear all, Is there a way to omit particles with zero charge from calculations for Coulomb-interactions or PME? In my calculations i want to coarse-grain my solvent, but the solute should be still represented by atoms. In doing so the solvent-molecules have a zero charge. I noticed that for a simulation with only the CG-solvent significant time was spent for the PME-part of the simulation. If i would simulate the complete system (atomic solute + coarse-grained solvent), i would save only time for the reduced number of particles (compared to atomistic solvent). But if i could omit the zero-charge solvent from the Coulomb-/PME-part, it would save much additional time. Is there an easy way for the omission, or would one have to hack the code? If the latter is true, how hard would it be and where do i have to look? (First idea would be to create an index-file group with all non-zero-charged particles and then run in the loops needed for Coulomb/PME only over this subset of particles.) I have only experience with Fortran and not with C++. Only other solution which comes to my mind would be to use plain cut-offs for the Coulomb-part. This would save time required for doing PME but will in turn cost time for the calculations of zeros (Coulomb-interaction for the CG-solvent). But more importantly would introduce artifacts from the plain cut-off :( Particles with zero charge are not included in neighbour lists used for calculating Coulomb interactions. The statistics in the M E G A -F L O P S A C C O U N T I N G section of the .log file will show that there is significant use of loops that do not have Coul component. So already these have no effect on half of the PME calculation. I don't know whether the grid part is similarly optimized, but you can test this yourself by comparing timing of runs with and without charged solvent. Mark Ok, i will test this. But here is the data i obtained for two simulations, one with plain cut-off and the other with PME. As one sees the simulation with plain cut-offs is much faster (by a factor of 6). Yes. I think I have seen this before for PME when (some grid cells) are lacking (many) charged particles. You will see that the nonbonded loops are always VdW(T) for tabulated VdW - you have no charges at all in this system and GROMACS has already optimized its choice of nonbonded loops accordingly. You would see Coul(T) + VdW(T) if your solvent had charge. It's not a meaningful test of the performance of PME vs cut-off, either, because there are no charges. Mark --- With PME: M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops --- VdW(T) 1132.029152 61129.574 0.1 Outer nonbonded loop1020.997718 10209.977 0.0 Calc Weights 16725.001338 602100.048
[gmx-users] Add counter-ions using virtual atom???
Hi, I'm getting better to use Gromacs owing to many posts on this sites :) . I have several questions about adding the counter-ions. My system has a number of N2 molecules which has charge, -0.40484(for single N) X 2. Thus, I have to add some counter-ions to make the system neutral. However, because I'm newbie on Gromacs, I thought of several clumsy ways myself. #1. Add virtual sites (virtual atoms) which has counter-ions like below. [ atomtypes ] ; name mass charge ptype sigma epsilon DUM 00.80968 V0.00.0 I set the coordinates of each virtual DUM atoms to the center of N2 molecules. #2. using genion in Gromacs. But, I have no idea on this. What molecules do I have to designate to charge plus ion using genion ?? I typed below line. genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g md_0_1_genion.log -p topol_genion.top -np 322 -pname dum -pq 0.80968 and selected N2 molecules which is diffusing particle. It results that the name of half of N2 molecules is changed as DUM. (maybe the system become neutral) The number of N2 molecules should be fixed. Do I have additional N2 molecule for charging using genion?? Then, what are the initial coordinates??? please help me any advises would be helpful. How can I do that??? -- 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] On g_hbond
Hi everyone! On this page http://manual.gromacs.org/online/g_hbond.html there is an option -r2 when using g_hbond. What is this r2? I can't find it in the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance which can be switched to H-A by using the -da no. Need help on what is -r2 (could this be for specifying a third criterion for the for distance O-H in addition to the angle cut-off and O-O distance cut-off). Thanks! Bernard-- 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] Add counter-ions using virtual atom???
Kiwoong Kim wrote: Hi, I'm getting better to use Gromacs owing to many posts on this sites :) . I have several questions about adding the counter-ions. My system has a number of N2 molecules which has charge, -0.40484(for single N) X 2. Thus, I have to add some counter-ions to make the system neutral. However, because I'm newbie on Gromacs, I thought of several clumsy ways myself. #1. Add virtual sites (virtual atoms) which has counter-ions like below. [ atomtypes ] ; name mass charge ptype sigma epsilon DUM 00.80968 V0.00.0 I set the coordinates of each virtual DUM atoms to the center of N2 molecules. #2. using genion in Gromacs. But, I have no idea on this. What molecules do I have to designate to charge plus ion using genion ?? I typed below line. genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g md_0_1_genion.log -p topol_genion.top -np 322 -pname dum -pq 0.80968 and selected N2 molecules which is diffusing particle. It results that the name of half of N2 molecules is changed as DUM. (maybe the system become neutral) The number of N2 molecules should be fixed. Do I have additional N2 molecule for charging using genion?? Then, what are the initial coordinates??? please help me any advises would be helpful. How can I do that??? I see no reason why you should do either. For dinitrogen, which has no net dipole, it seems intuitive to me that both N atoms should have zero charge. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] grompp g96angle types error
Dear all, I launch those commands for few models : pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p 2it7-10_bestene1mc-SC.top -ignh -missing editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 -c -bt cubic grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp and at the grompp command I obtain : checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file 2it7-10_bestene1mc-SC.top, line 1242]: No default G96Angle types Excluding 3 bonded neighbours for Protein 1 NOTE: System has non-zero total charge: 1.00e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 254 # G96ANGLES: 367 # PDIHS: 149 # IDIHS: 108 # LJ14: 436 I don't understand the meaning of: No default G96Angle types. All my files are generated by the same way, with the same softwares, and the sames options. All the models are done by the same software so the .pdb file only the coordinates of the protein change for one model to another. Can you help me? Thanks, Pierre THEVENET -- 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] grompp g96angle types error
pitheve...@free.fr wrote: Dear all, I launch those commands for few models : pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p 2it7-10_bestene1mc-SC.top -ignh -missing editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 -c -bt cubic grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp and at the grompp command I obtain : checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file 2it7-10_bestene1mc-SC.top, line 1242]: No default G96Angle types Excluding 3 bonded neighbours for Protein 1 NOTE: System has non-zero total charge: 1.00e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 254 # G96ANGLES: 367 # PDIHS: 149 # IDIHS: 108 # LJ14: 436 I don't understand the meaning of: No default G96Angle types. All my files are generated by the same way, with the same softwares, and the sames options. All the models are done by the same software so the .pdb file only the coordinates of the protein change for one model to another. Can you help me? The error message indicates that angle parameters do not exist in the chosen force field for a certain sequence of atoms. This would be highly unusual for a standard protein. Are you using any custom residues? The error message indicates the line in the .top that is causing the problem. Look it up, find which atoms it corresponds to, and check ffbonded.itp to verify that suitable parameters are indeed not present. If you're using some kind of custom residue or nonstandard composition of atoms, then you'll likely have to parameterize the missing term(s) yourself. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp g96angle types error
pitheve...@free.fr wrote: The problem seems to be between 3 S of CYS residues. I only use the 20 usual residues and with no modifications. An angle involving three S atoms? That should never occur. Where is the ffbonded.itp file? It's in $GMXLIB, i.e. the /share/gromacs/top subdirectory of your Gromacs installation. If the problematic angle is indeed S-S-S, I guarantee you won't find it there, though. -Justin Thank you, Pierre THEVENET - Mail original - De: Justin A. Lemkul jalem...@vt.edu À: Discussion list for GROMACS users gmx-users@gromacs.org Envoyé: Mardi 17 Janvier 2012 15:12:58 Objet: Re: [gmx-users] grompp g96angle types error pitheve...@free.fr wrote: Dear all, I launch those commands for few models : pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p 2it7-10_bestene1mc-SC.top -ignh -missing editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 -c -bt cubic grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp and at the grompp command I obtain : checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file 2it7-10_bestene1mc-SC.top, line 1242]: No default G96Angle types Excluding 3 bonded neighbours for Protein 1 NOTE: System has non-zero total charge: 1.00e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 254 # G96ANGLES: 367 # PDIHS: 149 # IDIHS: 108 # LJ14: 436 I don't understand the meaning of: No default G96Angle types. All my files are generated by the same way, with the same softwares, and the sames options. All the models are done by the same software so the .pdb file only the coordinates of the protein change for one model to another. Can you help me? The error message indicates that angle parameters do not exist in the chosen force field for a certain sequence of atoms. This would be highly unusual for a standard protein. Are you using any custom residues? The error message indicates the line in the .top that is causing the problem. Look it up, find which atoms it corresponds to, and check ffbonded.itp to verify that suitable parameters are indeed not present. If you're using some kind of custom residue or nonstandard composition of atoms, then you'll likely have to parameterize the missing term(s) yourself. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] grompp g96angle types error
Ok! The problem doesn't really come from gromacs so. It's my side-chain positioning software which made this... I'll try to fix it. Thank you very much. Pierre THEVEVENET - Mail original - De: Justin A. Lemkul jalem...@vt.edu À: Discussion list for GROMACS users gmx-users@gromacs.org Envoyé: Mardi 17 Janvier 2012 15:30:08 Objet: Re: [gmx-users] grompp g96angle types error pitheve...@free.fr wrote: The problem seems to be between 3 S of CYS residues. I only use the 20 usual residues and with no modifications. An angle involving three S atoms? That should never occur. Where is the ffbonded.itp file? It's in $GMXLIB, i.e. the /share/gromacs/top subdirectory of your Gromacs installation. If the problematic angle is indeed S-S-S, I guarantee you won't find it there, though. -Justin Thank you, Pierre THEVENET - Mail original - De: Justin A. Lemkul jalem...@vt.edu À: Discussion list for GROMACS users gmx-users@gromacs.org Envoyé: Mardi 17 Janvier 2012 15:12:58 Objet: Re: [gmx-users] grompp g96angle types error pitheve...@free.fr wrote: Dear all, I launch those commands for few models : pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p 2it7-10_bestene1mc-SC.top -ignh -missing editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 -c -bt cubic grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp and at the grompp command I obtain : checking input for internal consistency... calling /lib/cpp... processing topology... Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file 2it7-10_bestene1mc-SC.top, line 1242]: No default G96Angle types Excluding 3 bonded neighbours for Protein 1 NOTE: System has non-zero total charge: 1.00e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # G96BONDS: 254 # G96ANGLES: 367 # PDIHS: 149 # IDIHS: 108 # LJ14: 436 I don't understand the meaning of: No default G96Angle types. All my files are generated by the same way, with the same softwares, and the sames options. All the models are done by the same software so the .pdb file only the coordinates of the protein change for one model to another. Can you help me? The error message indicates that angle parameters do not exist in the chosen force field for a certain sequence of atoms. This would be highly unusual for a standard protein. Are you using any custom residues? The error message indicates the line in the .top that is causing the problem. Look it up, find which atoms it corresponds to, and check ffbonded.itp to verify that suitable parameters are indeed not present. If you're using some kind of custom residue or nonstandard composition of atoms, then you'll likely have to parameterize the missing term(s) yourself. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Cytochrom C
According your help and pdb2gmx -his -missing I could create input files. Also I used grompp without error. However, for mdrun I got this error: *Function type CMAP Dih. not implemented in ip_pert* How can I figure it out? Thanks, Dariush On Tue, Jan 10, 2012 at 4:37 PM, Krzysztof Kuczera kkucz...@ku.edu wrote: Hi Dariush If you are using the CHARMM27 force field, then all topology and parameters are in your share/top/charmm27.ff directory The defined molecules are listed in aminoacids.rtp and force field parameters in numerous other files. CHARMM does not use 'HIS' for histidine, but has HSD, HSE and HSP for the isomers with hydrogen at ND1, NE2 and both. You can either set these isomers by hand - by editing your PDB file or use the 'pdb2gmx -his' option for interactive definition. The bonus of keeping 'HIS' names and interactive setup is that bonds to heme iron will be generated based on the 'specbond.dat' entries, if HIS NE2 nitrogens are close enough to the FE. Krzysztof On 1/10/12 2:40 PM, Dariush Mohammadyani wrote: Does anybody know where can I find [ HIS ] parameters? Thanks, Dariush On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani d.mohammady...@gmail.com wrote: Dear Peter and Krzyszto, Thank you. I am following your comments. If I get any problem I will come back. On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai p...@uab.edu wrote: He must be using an older version of Gromacs. 4.5.4 and lower don't have ACE in charmm27. On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote: Here is the blocking group from gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp KK [ ACE ] [ atoms ] CH3 CT3 -0.270 0 HH31HA 0.090 1 HH32HA 0.090 2 HH33HA 0.090 3 C C 0.510 4 O O -0.510 5 [ bonds ] C CH3 C +N CH3 HH31 CH3 HH32 CH3 HH33 O C [ impropers ] C CH3 +N O On 1/6/12 12:40 PM, Peter C. Lai wrote: Corrected bonds section (sorry been up all night) [ ACE ] [ atoms ] CH3CT3-0.270 HH31 HA 0.091 HH32 HA 0.092 HH33 HA 0.093 CC 0.514 OO -0.515 [ bonds ] CH3HH31 CH3HH32 CH3HH33 CH3C C O Surprisingly, an .hdb entry for ACE exists so you don't need to create one. (and the .hdb entry uses HH3 as the base hydrogen name in ACE) On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote: Gromos96 53A6 has it. On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote: I tried charmm27 too. Error: Residue 'ACE' not found in residue topology database I tried all forcefield in the list provided by pdb2gmx, but non of them works. Dariush On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamersrjham...@wisc.edu wrote: HEME is in the charmm27 force field. bob h. On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: Yes, I have PDB file (1HRC.pdb). However, when I try to use pdb2gmx I get this error: Residue 'HEM' not found in residue topology database and HEM is Iron ion inside this protein. I do not know which forcefield is proper to use. I also tried MARTINI force field according their website; I used martinize.py script; Again I got error. Regards, Dariush On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkuljalem...@vt.edu wrote: Dariush Mohammadyani wrote: Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? There are several in the PDB. -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 %28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Robert J. Hamers Wisconsin Distinguished Professor Univ. of Wisconsin-Madison 1101 University Avenue Madison, WI 53706 Ph: 608-262-6371 Web: http://hamers.chem.wisc.edu -- Kind Regards, Dariush
Re: [gmx-users] Cytochrom C
Dariush Mohammadyani wrote: According your help and pdb2gmx -his -missing I could create input files. Also I used grompp without error. However, for mdrun I got this error: Using the -missing flag is very dangerous. If you're using it to override warnings or errors that pdb2gmx is giving, your simulations will almost certainly be junk because the topology is broken. *Function type CMAP Dih. not implemented in ip_pert* How can I figure it out? Without seeing your .mdp file and knowing which Gromacs version you're using, there's little anyone can do to help you. The error suggests you're trying to transform a CMAP dihedral using the free energy code, which cannot be done (per the error message). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Can I fix atoms and apply load to another atoms?
Hi guys, I have question about gromacs. I am doing SMD using gromacs and I don't know if gromacs can do this simulation: fixing atoms and applying load to another atoms at the same time? if yes how, if no what another programs can do it? Thanks, Talal -- 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] non-bonded [exclusions] / [ pairs ] for 56A_CARBO implementation
Hi, I'm still a bit confused about the [ pairs ] and [ exclusions ] sections of an .itp file. How would the procedure be if I want to change the Lennard-Jones parameters for certain pairs of atoms in a molecule? The reason I ask is that I have created a trehalose topology based on the 56A_CARBO (Hansen Hünenberger, 2011) parameters, but I'm a bit unsure that I got the special 1-5 and and 1-4 pair right. This is how I did it (the modified forcefield is G53A6 or G54A7): 1. Excluded the pairs by putting them in the [ exclusions ] section 2. Added the excluded pairs in the [ pairs ] section with function type 1 followed by the C6 and C12 parameters. Something like this: [ exclusions ] 15 [ pairs ] ;ft C6C12 15 1 0.22617E-020.74158E-06 Is the choice of function right? In the manual it looks like I could also use function type 3 here. What is more correct? Regards Jon Kapla -- _ Jon Kapla Division of Physical Chemistry Dpt. of Materials and Environmental Chemistry (MMK) Arrhenius Laboratory Stockholm University SE-106 91 Stockholm Pos:PhD Student Phone: +46 8 16 11 79 (office) Phone: +46 70 304 19 89 (cell) E-mail: jon.ka...@mmk.su.se _ -- 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] Re: Problem with trjconv and centering bilayer.
Ioannis Beis wrote: Quoting gmx-users-requ...@gromacs.org: Message: 2 Date: Mon, 16 Jan 2012 13:38:11 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Problem with trjconv and centering bilayer. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f146e93.4090...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed Ioannis Beis wrote: Dear gromacs users, I am trying to center the trajectory of a bilayer in the rectangular simulation box in the frame of my effort to calculate the bilayer thickness with g_dist. According to the visualization, the upper layer of the membrane lies on the lowest part of the box and the lower part of the membrane on the highest part of the box, with the water in the middle. There should not be anything wrong with drifting along the z-axis, since the initial structure was at the very bottom of the box, so even a small drift downwards -due to the pbc- would place the lower part of the membrane on the top of the box. I tried issuing: trjconv -f my_trajectory.xtc -s my_initial_structure.gro -o my_trajectory_no_jump.xtc -pbc nojump with 0 (for system) and subsequently trjconv -f my_trajectory_no_jump.xtc -s DOPC_1DOG.tpr -o my_trajectory_no_jump_center.xtc -center -boxcenter tric -pbc mol with 1 (other) for centering and 0 (system) for output. I used this kind of commands some time ago and they worked fine. Now strangely the bilayer remains around the position that I described in the beginning. Is it possible that the program treats the bilayer separated as it looks in vmd and considers the geometrical center in the middle of the water instead of the middle of the bilayer? That's exactly what it does. I tried the -trans flag to translate the bilayer along z-axis near the center and repeated the steps, but the new trajectory wasn't even visible in vmd. In addition, the .gro files generated by trjconv are apparently trajectory files instead of structure files. I don't feel confident about using editconf for operations like translation of a single initial structure, because as far as I understand editconf is a tool meant mostly for setting up systems; thus I was sceptical about messing a structure with editconf that I would later on use together with an .xtc file as input for trjconv. However, trjconv doesn't seem to generate structure output files. I don't understand the meaning of a .gro file as trajectory file since there are already at least 3 file formats for trajectories. Generally speaking, a trajectory is just a series of coordinates, so you can output it into a number of formats, including .gro and .pdb, among others. You get a chain of coordinate files that may (or may not) end up being useful in some applications. So how can I bring my bilayer's trajectory in the center of the unit cell for reliable thickness calculation without drifts? Is it possible at the same time to have clear visualization without disturbances? trjconv with -pbc mol still gives rise to lines in the visualization, apparently as a result of atom jumps. Sadly trajectory files cannot be inspected and visualization is quite handy for certain types of feedback in various data analysis-related tasks, so it would be nice if the trajectories used for analysis also look proper in vmd. I can think of two approaches, the first of which I have used so it should work ;) 1. Provide a custom index group specifying only a single lipid atom from the end of a hydrocarbon chain and center on it. Therefore, its geometric center has to be the center of the box, and it should bring the rest of the membrane to the (visual) center of the unit cell. 2. Calculate the distance with the trajectory you have now, and subtract it from the z-length (assuming the membrane plane is x-y) of the box (stored in the .edr file). First of all thank you very much for the reply. To make sure there is not something that I misunderstand about how trjconv works, I would like to mention what I did and how I anticipate it. I made the index file with a last carbon from a random acyl chain and issued: trjconv -f my_init_traj.xtc -o towards_center_traj.xtc -pbc mol -center -boxcenter tric -n tip_atom.ndx How did this work? The use of -pbc implies the need for -s. with centering at the index file atom and then: trjconv -f towards_center_traj.xtc -s my_binary.tpr -o centered_traj.xtc -pbc mol -center -boxcenter tric If properly centered, this step should not be required. with centering at the middle of the bilayer. The final .xtc output is to be used as input in the g_dist. I assume that .tpr is used only for the masses of the atoms (so we are talking about a mass-weighted geometrical center, which isn't mentioned in the manual). Therefore it is mandatory in the second command, but not in the first. Is this going to give the correct result? Masses are not used for centering; it is a simple coordinate transformation.
Re: [gmx-users] Cytochrom C
Dear Justin, You are right, I had some warning and with -missing I override them, e.g.: WARNING: atom HA is missing in residue HEM 105 in the pdb file WARNING: atom HB is missing in residue HEM 105 in the pdb file ... 30 missing atoms. I did not know how should figure them out. I am using GROMACS 4.5.3 and charmm27.ff. Cytochrome C is a difficult protein to simulate :( Thanks, Dariush On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul jalem...@vt.edu wrote: Dariush Mohammadyani wrote: According your help and pdb2gmx -his -missing I could create input files. Also I used grompp without error. However, for mdrun I got this error: Using the -missing flag is very dangerous. If you're using it to override warnings or errors that pdb2gmx is giving, your simulations will almost certainly be junk because the topology is broken. *Function type CMAP Dih. not implemented in ip_pert* How can I figure it out? Without seeing your .mdp file and knowing which Gromacs version you're using, there's little anyone can do to help you. The error suggests you're trying to transform a CMAP dihedral using the free energy code, which cannot be done (per the error message). -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/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
Re: [gmx-users] Cytochrom C
Dariush Mohammadyani wrote: Dear Justin, You are right, I had some warning and with -missing I override them, e.g.: WARNING: atom HA is missing in residue HEM 105 in the pdb file WARNING: atom HB is missing in residue HEM 105 in the pdb file ... 30 missing atoms. I did not know how should figure them out. I am using GROMACS 4.5.3 and charmm27.ff. Cytochrome C is a difficult protein to simulate :( You'll make your life more difficult by overriding error messages you don't understand ;) If all of the missing atoms are hydrogens, then a suitable .hdb entry must be constructed for the heme group so that the H atoms are all rebuilt. Alternatively, you can add them with some external modeling software capable of such tasks. If there are other missing atoms, they too need to be added. You must begin with an intact model, or otherwise have the ability to produce one. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Abot genbox and editcon
Dear justin Thank you for your previous reply I have solvated my protein molecule with specific number of water molecules By keeping the protein (solute) at center of box (option available in editconf) but when i visualize the resultant .gro file in VMD the solute molecule are not closely surrounded by water moleculesi need Solute molecules to be closely surrounded by solvent molecules without changing the dimension of box i am using Cubic box is there is any option in available in gromacs With Cheers S.vidhyasankar Thanks in advance-- 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] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values
Hi users, Am trying to run the grimaces gpu version. I receive an error while doing the nvt step . my nvt.mdp file goes like this= ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, volume and temperature) cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 1250 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 1; Write every step to the log nstenergy= 5; Write energies at every step nstxtcout= 0; Do not write a compressed trajectory energygrps = System ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 0.9 epsilon_rf = 54 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling tcoupl = Berendsen tc-grps = System tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = hbonds i get an error as Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values please tell me whats wrong. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values
aiswarya pawar wrote: Hi users, Am trying to run the grimaces gpu version. I receive an error while doing the nvt step . my nvt.mdp file goes like this= ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, volume and temperature) cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 1250 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 1; Write every step to the log nstenergy= 5; Write energies at every step nstxtcout= 0; Do not write a compressed trajectory energygrps = System ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 0.9 epsilon_rf = 54 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling tcoupl = Berendsen tc-grps = System tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDS constraints = hbonds i get an error as Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values please tell me whats wrong. Precisely what it says. You specify one group to be coupled (System), but then provide coupling information for two groups. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] walls
Dear Gromacs users, May I ask you to help me about use of walls in martini coarse-grained, please? I defined two walls for my system as following: pbc = xy nwall = 2 wall_type = 12_6 wall_r_linpot = 1 wall_atomtype = W W I selected water as wall_atomtype, when I run grompp, all of things are good, but when I run mdrun, system give me: Segmentation fault If I use pbc=xyz without walls, all of things are good, then my problem is wall. May I know my mistake, please? Best Regards Sara -- 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] query about identifying representative snapshots from a 2D FEL
Dear Gromacs users I am interested in identifying the representative snapshots from a 2D Free energy landscape plot generated using g_sham using the reaction coordinates obtained from EV1 and EV2 projections. Can some suggest on how to back trace the coordinates from a 2D FEL and also the time. To be more precise i want to carry out an analysis exactly like what has been reported in Figure 8 of this refereed paper http://pubs.rsc.org/en/content/articlehtml/2011/cp/c0cp02697b Your suggestions would be greatly appreciated Thanking you in advance Regards Vijayan.R -- 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] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values
Yes it worked. Thanks :) On Tue, Jan 17, 2012 at 10:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Hi users, Am trying to run the grimaces gpu version. I receive an error while doing the nvt step . my nvt.mdp file goes like this= ; VARIOUS PREPROCESSING OPTIONS title= NVT simulation (constant number, volume and temperature) cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 1250 ; OUTPUT CONTROL OPTIONS nstxout = 0; No output, except for last frame (coordinates) nstvout = 0; No output, except for last frame (velocities) nstfout = 0; No output, except for last frame (forces) nstlog = 1; Write every step to the log nstenergy= 5; Write energies at every step nstxtcout= 0; Do not write a compressed trajectory energygrps = System ; Write energy information separately for these groups ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 0.9 epsilon_rf = 54 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling tcoupl = Berendsen tc-grps = System tau_t= 0.1 0.1 ref_t= 300 300 ; Pressure coupling pcoupl = no ; OPTIONS FOR BONDSconstraints = hbonds i get an error as Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values please tell me whats wrong. Precisely what it says. You specify one group to be coupled (System), but then provide coupling information for two groups. -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/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] COMETS 2012 - 3rd IEEE Track on Collaborative Modeling and Simulation - Call for Papers
(Please accept our apologies if you receive multiple copies of this message) # IEEE WETICE 2012 3rd IEEE Track on Collaborative Modeling and Simulation (Comets 2012) in cooperation with AFIS (INCOSE France Chapter) MIMOS (Italian Association for MS) CALL FOR PAPERS # June 25-27, 2012, Toulouse (France) http://www.sel.uniroma2.it/comets12 # # Papers Due: March 16, 2012 # Accepted papers will be published in the conference proceedings # by the IEEE Computer Society Press and indexed by EI. # Modeling and Simulation (MS) is increasingly becoming a central activity in the design of new systems and in the analysis of existing systems because it enables designers and researchers to investigate systems behavior through virtual representations. For this reason, MS is gaining a primary role in many industrial and research fields, such as space, critical infrastructures, manufacturing, emergency management, biomedical systems and sustainable future. However, as the complexity of the investigated systems increases and the types of investigations widens, the cost of MS activities increases for the more complex models and for the communications among a wider number and variety of MS stakeholders (e.g., sub-domain experts, simulator users, simulator engineers, and final system users). To address the increasing costs of MS activities, collaborative technologies must be introduced to support these activities by fostering the sharing and reuse of models, by facilitating the communications among MS stakeholders, and more generally by integrating processes, tools and platforms. Aside from seeking applications of collaborative technologies to MS activities, the track seeks innovative contributions that deal with the application of MS practices to the design of collaborative environments. These environments are continuously becoming more complex, and therefore their design requires systematic approaches to meet the required quality of collaboration. This is important for two reasons: to reduce rework activities on the actual collaborative environment, and to maximize the productivity and the quality of the process the collaborative environment supports. MS offers the methodologies and tools for such investigations and therefore it can be used to improve the quality of collaborative environments. A non–exhaustive list of topics of interest includes: * collaborative environments for MS * collaborative Systems of Systems MS * workflow modelling for collaborative environments and processes * agent-based MS * collaborative distributed simulation * collaborative component-based MS * net-centric MS * web-based MS * model sharing and reuse * model building and evaluation * modeling and simulation of business processes * modeling for collaboration * simulation-based performance evaluation of collaborative networks * model-driven simulation engineering * domain specific languages for the simulation of collaborative environments * domain specific languages for collaborative MS * databases and repositories for MS * distributed virtual environments * virtual research environment for MS * collaborative DEVS MS To stimulate creativity, however, the track maintains a wider scope and invites interested researchers to present contributions that offer original perspectives on collaboration and MS. +++ On-Line Submissions and Publication +++ CoMetS'12 intends to bring together researchers and practitioners to discuss key issues, approaches, open problems, innovative applications and trends in the track research area. This year, we will accept submissions in two forms: (1) papers (2) poster and industrial presentations (1) Papers should contain original contributions not published or submitted elsewhere. Papers up to six pages (including figures, tables and references) can be submitted. Papers should follow the IEEE format, which is single spaced, two columns, 10 pt Times/Roman font. All submissions should be electronic (in PDF) and will be peer-reviewed by at least three program committee members. Accepted full papers will be included in the proceedings and published by the IEEE Computer Society Press (IEEE approval pending). Please note that at least one author for each accepted paper should register to attend WETICE 2012 (http://www.wetice.org) to have the paper published in the proceedings. (2) Posters should describe a practical, on-the-field, experience in any domain area using collaborative MS. The poster submission requires the submission of an abstract for evaluation from the
[gmx-users] questions on distance restraints
Dear gmxusers, I have some questions about distance restraints that I hope you would be able to shed some light on. Thanks in advance. I am trying to apply distance restraints to my protein. Below was what I did: -use genrestr to create my ca_disre.itp genrestr -f membedded_em.gro -o ca_disre.itp -disre (pop-up prompt: CA atoms selected) -in my mdp file I added this line near the top: define = -DDISRES -my top file looks like that ; Include forcefield parameters #include gromos53a6_lipid.ff/forcefield.itp ;Include Protein Topology #include A2a.itp ; Include Position restraint file #ifdef DISRES #include ca_disre.itp #endif ; #ifdef POSRES #include posre.itp #endif ; ;Include POPC topology #include popc.itp #ifdef LIPID_POSRES #include lipid_posre.itp #endif ;Include water topology #include gromos53a6_lipid.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos53a6_lipid.ff/ions.itp [ system ] ; Name Protein and POPC and Water [ molecules ] ; Compound#mols Protein_chain_X 1 POPC 327 SOL 24767 CL 11 The simulation ran without a problem. However, after it was completed, I compared the final protein structure with the initial and it looked like the atoms (even the CA atoms , especially those in the loops) had moved quite a fair bit away from the original position. This made me wonder if the distance restraints had indeed been applied or perhaps the force constant was not large enough (default =1000 kJ/mol/nm^2)? I had checked the mdout.mdp file define = -DDISRES was there... wasn't sure how else I could check this. To test whether it was due to the latter, I had tried rerunning the simulation for 1ns simulation with disre_fc= 1 added to the mdp file. This time the atoms did not move as far away as previously observed. I have tried google-ing for the proper way to impose distance restraints but didn't find my searches too useful. I wonder if anyone could confirm with me that the above method is correct/ tell me that I had done something wrong. Cheers for that! Best wishes, Huiwen This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- 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] GROMOS 53A6 AND charmm36.ff
Hi all, I want to use the GROMOS 53A6 forcefield for the protein, water, ions. For the membrane I intend to use charmm36.ff. I downloaded the charmm36.ff and put the folder as a sub-folder in /sw/share/gromacs/top/ as suggested in the GROMACS manual. When I go: pdb2gmx -f test.pdb -o -p -i -ignh -ff charmm I get: Fatal error: Library file ffcharmm.ff.rtp not found in current dir nor in default directories. So, I renamed lipids.rtp in the charmm36.ff folder to fflipids.rtp and moved the file into /sw/share/gromacs/top/ and now I get around that issue, but get a new error message: Fatal error: Library file fflipids.atp not found in current dir nor in default directories. And it's not obvious to me which of the files in the charmm36.ff folder this corresponds to? I guess my question is how to use pdb2gmx with he GROMOS 53A6 forcefield AND the charmm36.ff forcefield? Best regards / Magnus Andersson === Magnus Andersson, PhD Department of Physiology and Biophysics University of California, Irvine Irvine, CA 92697-4560 (949) 824-6993 Fax: (949) 824-8540 === -- 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] GROMOS 53A6 AND charmm36.ff
Magnus Andersson wrote: Hi all, I want to use the GROMOS 53A6 forcefield for the protein, water, ions. For the membrane I intend to use charmm36.ff. I downloaded the charmm36.ff and put the folder as a sub-folder in /sw/share/gromacs/top/ as suggested in the GROMACS manual. When I go: pdb2gmx -f test.pdb -o -p -i -ignh -ff charmm I get: Fatal error: Library file ffcharmm.ff.rtp not found in current dir nor in default directories. So, I renamed lipids.rtp in the charmm36.ff folder to fflipids.rtp and moved the file into /sw/share/gromacs/top/ and now I get around that issue, but get a new error message: Fatal error: Library file fflipids.atp not found in current dir nor in default directories. It seems like you're using an old (pre-4.5) version of Gromacs. The force field organization is completely different, so what you're trying to do won't work unless you upgrade to a new version. And it's not obvious to me which of the files in the charmm36.ff folder this corresponds to? I guess my question is how to use pdb2gmx with he GROMOS 53A6 forcefield AND the charmm36.ff forcefield? You can't. The functional forms, representations of atoms, combination rules, etc. are different. Even if you could somehow hack the force fields together to make it work, I would suspect any reviewer would immediately throw out the results in the absence of some pretty impressive demonstration that what you're trying to do will actually give a reasonable physical model. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] questions on distance restraints
Hi Huiwen, Your approach seems good. Information about the distance restraints will be printed in the log file from mdrun, or can be extracted from the .edr file. You can also work your way through the information in the .tpr file given by gmxdump to see if they are indeed properly defined. Cheers, Tsjerk On Jan 18, 2012 1:46 AM, NG HUI WEN huiwen...@nottingham.edu.my wrote: Dear gmxusers, ** ** I have some questions about distance restraints that I hope you would be able to shed some light on. Thanks in advance. ** ** I am trying to apply distance restraints to my protein. Below was what I did: ** ** -use genrestr to create my ca_disre.itp genrestr –f membedded_em.gro –o ca_disre.itp –disre (pop-up prompt: CA atoms selected) ** ** -in my mdp file I added this line near the top: define = -DDISRES ** ** -my top file looks like that ; Include forcefield parameters #include gromos53a6_lipid.ff/forcefield.itp ** ** ;Include Protein Topology #include A2a.itp ** ** ; Include Position restraint file #ifdef DISRES #include ca_disre.itp #endif ; #ifdef POSRES #include posre.itp #endif ; ** ** ;Include POPC topology #include popc.itp #ifdef LIPID_POSRES #include lipid_posre.itp #endif ** ** ;Include water topology #include gromos53a6_lipid.ff/spc.itp ** ** #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ** ** ; Include topology for ions #include gromos53a6_lipid.ff/ions.itp ** ** [ system ] ; Name Protein and POPC and Water ** ** [ molecules ] ; Compound#mols Protein_chain_X 1 POPC 327 SOL 24767 CL 11 ** ** The simulation ran without a problem. However, after it was completed, I compared the final protein structure with the initial and it looked like the atoms (even the CA atoms , especially those in the loops) had moved quite a fair bit away from the original position. This made me wonder if the distance restraints had indeed been applied or perhaps the force constant was not large enough (default =1000 kJ/mol/nm^2)? I had checked the mdout.mdp file “define = -DDISRES” was there… wasn’t sure how else I could check this. ** ** To test whether it was due to the latter, I had tried rerunning the simulation for 1ns simulation with “disre_fc= 1” added to the mdp file. This time the atoms did not move as far away as previously observed. ** ** I have tried google-ing for the proper way to impose distance restraints but didn’t find my searches too useful. I wonder if anyone could confirm with me that the above method is correct/ tell me that I had done something wrong. ** ** Cheers for that! ** ** Best wishes, Huiwen ** ** ** ** This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- 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] Regarding trajectory file
Dear All, I have ran a 10 ns production run for chloranil in 500 methanol solvent box. I want to get the coordinates of solvent and solute at different time steps from the trajectory file (*.xtc). Can anybody tell me how to extract the details using VMD or any other viewer. Thank you in advance *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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] Regarding trajectory file
On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote: Dear All, I have ran a 10 ns production run for chloranil in 500 methanol solvent box. I want to get the coordinates of solvent and solute at different time steps from the trajectory file (*.xtc). Can anybody tell me how to extract the details using VMD or any other viewer. You're unlikely to get help for non-GROMACS software on this mailing list. Check out manual section 7.4 for clues on what GROMACS tools might help, and then section 8 and appendix D for more details. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding trajectory file
You can write this on VMD forum. Anyways you can try by doing this in the
Tcl console-
set sel [atomselect top solvent]
$sel get {x y z}
This would give you the coordinates of the solvent, for your purpose you
got to iterate so as to get for each time step.
Aiswarya
SERC Dept, IISc
Bangalore
On Wed, Jan 18, 2012 at 12:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote:
Dear All,
I have ran a 10 ns production run for chloranil in 500
methanol solvent box. I want to get the coordinates of solvent and solute
at different time steps from the trajectory file (*.xtc). Can anybody tell
me how to extract the details using VMD or any other viewer.
You're unlikely to get help for non-GROMACS software on this mailing list.
Check out manual section 7.4 for clues on what GROMACS tools might help,
and then section 8 and appendix D for more details.
Mark
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