[gmx-users] About Index Files
Dear Justin Thanks you for your Previous reply I am Following your Lipid Protein Tutorial When I try to create index File from .gro file obtained After genion EM (grompp) pro gramme Then I have got Repetition of Groups (from 1 to 11 11 to 21) in Command prompt 0 System : 15392 atoms 1 Protein : 714 atoms 2 Protein-H : 462 atoms 3 C-alpha : 42 atoms 4 Backbone : 126 atoms 5 MainChain : 168 atoms 6 MainChain+Cb : 210 atoms 7 MainChain+H : 210 atoms 8 SideChain : 504 atoms 9 SideChain-H : 294 atoms 10 Prot-Masses : 714 atoms 11 non-Protein : 14678 atoms 12 Protein : 714 atoms 13 Protein-H : 462 atoms 14 C-alpha : 42 atoms 15 Backbone : 126 atoms 16 MainChain : 168 atoms 17 MainChain+Cb : 210 atoms 18 MainChain+H : 210 atoms 19 SideChain : 504 atoms 20 SideChain-H : 294 atoms 21 Prot-Masses : 714 atoms 22 non-Protein : 14678 atoms 23 Other : 6250 atoms 24 DPPC : 6250 atoms 25 NA : 1 atoms 26 Water : 8427 atoms 27 SOL : 8427 atoms 28 non-Water : 6965 atoms 29 Ion : 1 atoms 30 DPPC : 6250 atoms 31 NA : 1 atoms 32 Water_and_ions : 8428 atoms I do not Know Why This Happens? Could You Please Suggest Any Solution? 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
Re: [gmx-users] Diffusion beyond periodic boundary
Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the distance from pdb file. However, when the particle goes beyond periodic boundary, the x-y-z coordination is rewind into the box size. So, the dislocated distance is wrong. Could you please tell me how to calculate the dislocated distance accurately ? Best regards Kenji -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] 4.6 seems improved the efficiency
Hello : I found the new released 4.6 probably improved very obviously for the efficiency. With the same system, I used 4.5.5 it can get 26 ns/day (144 CPU, 55,000 atoms, Amber FF) with g_tume_pme optimization. Now I used 4.6, even without g_tune_pme, the pme mesh/force can get 0.8-1.0 with efficiency 32 ns/day. That's really nice. I don't know whether other users have similar experiences for this new version. Albert -- 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] Diffusion beyond periodic boundary
Dear Tsjerk Thank you very much, -pbc nojump works well. Is it possible to select the specific molecule for -pbc nojump ? For example, the coordinates of water molecules are rewind and the LJ particles are NOT rewind ? Regards Kenji - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: 2013-02-09 17:24:23 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the distance from pdb file. However, when the particle goes beyond periodic boundary, the x-y-z coordination is rewind into the box size. So, the dislocated distance is wrong. Could you please tell me how to calculate the dislocated distance accurately ? Best regards Kenji -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- 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] Diffusion beyond periodic boundary
Hi Kenji, That's not possible. But why would you need that? It's not very hard to make the changes required in gmx_trjconv.c Cheers, Tsjerk On Sat, Feb 9, 2013 at 9:37 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear Tsjerk Thank you very much, -pbc nojump works well. Is it possible to select the specific molecule for -pbc nojump ? For example, the coordinates of water molecules are rewind and the LJ particles are NOT rewind ? Regards Kenji - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: 2013-02-09 17:24:23 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the distance from pdb file. However, when the particle goes beyond periodic boundary, the x-y-z coordination is rewind into the box size. So, the dislocated distance is wrong. Could you please tell me how to calculate the dislocated distance accurately ? Best regards Kenji -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] Re: Reference structure for PCA.
Any comments/help on this query. I am stuck with this. Thanks, -Vivek. On Thu, Feb 7, 2013 at 1:26 PM, vivek modi modi.vivek2...@gmail.com wrote: Hello, I have troubled you with a similar question before also, but I guess I need some more clarification. My question is about the reference structure in PCA analysis. I have 100ns long protein simulation which I want to analyze using PCA. The RMSD shows fluctuations upto initial 25-30ns and then becomes very stable. I have performed PCA on the last 30ns window of the simulation where I assume the simulation has converged (I also did on other time windows as well). The question is this: I did the analysis on the last 30ns window in two ways by taking two different reference structures. a. I take the average structure of the trajectory (0-100ns) as the reference and then do the fitting and calculate covariance matrix for last 30ns. This is done because I suspect that the average structure over full trajectory will reflect all the changes occurring in the protein. It also gives me low cosines (0.1). The PCs show movement occurring in certain regions of the protein. b. I take the average structure from the same window (last 30ns) then do the fitting and calculate covariance matrix for the same. This is done with an assumption that the reference structure must reflect the equilibriated/stable part of the trajectory unlike the previous case. Surprisingly it gives me high cosines (0.5). Unlike the previous case, this method shows very small movement in the protein (very low RMSF). Both of these methods give me different RMSF for the PCs although they are done on the same part of the trajectory but the reference structure is influencing the output. Which protocol among the two is appropriate ? And how can we explain high cosines in second case where the reference structure is the average of the same time window (there must not be large deviation) while I get low cosine for the first case where deviations are calculated from the full trajectory average (large deviation) ? Any help is appreciated. Thanks, -Vivek Modi Graduate Student IITK. -- 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] Water models and diffusion coefficient
On 2013-02-09 14:21, Joinforfun Doe wrote: Hello, I am simulating a model of heavy water, with charges modified from SPCE model. This was proposed by Grigera [2001], with H replaced by D and charges on O and H increased from values proposed in SPCE model. I have verified by using gmxdump that gromacs sees the mass of H as 2.014 amu and the charges as specified in the topology file. The density comes out as expected for heavy water. The system equilibrates well (well-defined fluctutations, no trends in energy, density, pressure, temperature) However, the diffusion coefficient is always lower than that expected for the model. By using the same parameter files I ran a simulation for normal water (SPCE) model and the diffusion coefficient matches with that reported from other simulations. Is there something else that I should check? or is there something about g_msd that I am missing? Any pointers would be really helpful. Thanks Most water models have too high D. (see J Chem Phys 108 pp. 10220-10230 (1998)). SPC/E is about right. However that is more luck than skill so to speak, since there still is a lot of physics missing from this extremely simple model. So if you can reproduce literature values for the model and some experimental data, dens, DHvap, then this is as good as it gets. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.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] Diffusion beyond periodic boundary
Dear Tsjerk Thank you for reply. I will make PDB using -pbc nojump and rewind only the selected molecules by own program. Thank you Kenji - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: 2013-02-09 19:17:12 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, That's not possible. But why would you need that? It's not very hard to make the changes required in gmx_trjconv.c Cheers, Tsjerk On Sat, Feb 9, 2013 at 9:37 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear Tsjerk Thank you very much, -pbc nojump works well. Is it possible to select the specific molecule for -pbc nojump ? For example, the coordinates of water molecules are rewind and the LJ particles are NOT rewind ? Regards Kenji - Original Message - From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: 2013-02-09 17:24:23 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the distance from pdb file. However, when the particle goes beyond periodic boundary, the x-y-z coordination is rewind into the box size. So, the dislocated distance is wrong. Could you please tell me how to calculate the dislocated distance accurately ? Best regards Kenji -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 -- 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] Re: Water models and diffusion coefficient
Thanks for your reply David. However, what I am concerned is that with the parameters, q[O] = -0.870, and q[H] = 0.435, the original author reported diffusion coefficient very close to 2.0 e-5 cm^2/s. My values for even much longer simulations (200 ns after 1ns each of NVT and NPT equilibration) reports diffusion coefficients which are always much lesser ( in the range 1.4 - 1.5 e-5 cm^2/s). I was wondering if there is something that I should understand better about g_msd not getting the right mass of H atoms? -- View this message in context: http://gromacs.5086.n6.nabble.com/Water-models-and-diffusion-coefficient-tp5005377p5005380.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Water models and diffusion coefficient
What time period do you use to fit the mean-squared displacement to determine the diffusion coefficient? g_msd determines the diffusion coefficient by performing a linear fit over the time interval specified by the -beginfit and -endfit flags, which default to 10% and 90% of the simulation time (if I remember correctly) if you do not specify values. If your mean-squared displacement is not linear over this interval, then you could have a very poor estimate of the diffusion coefficient. You might to look at the plots of the MSD generated to see if it is linear over the interval you fit; if it plateaus over this period then likely the diffusion coefficient is an underestimate, and since the value you measure is relatively close to the literature value then that could explain the lower value. - Reid On Sat, Feb 9, 2013 at 9:12 AM, learnmd joinforfun8...@gmail.com wrote: Thanks for your reply David. However, what I am concerned is that with the parameters, q[O] = -0.870, and q[H] = 0.435, the original author reported diffusion coefficient very close to 2.0 e-5 cm^2/s. My values for even much longer simulations (200 ns after 1ns each of NVT and NPT equilibration) reports diffusion coefficients which are always much lesser ( in the range 1.4 - 1.5 e-5 cm^2/s). I was wondering if there is something that I should understand better about g_msd not getting the right mass of H atoms? -- View this message in context: http://gromacs.5086.n6.nabble.com/Water-models-and-diffusion-coefficient-tp5005377p5005380.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 -- Reid Van Lehn NSF/MIT Presidential Fellow Alfredo Alexander-Katz Research Group Ph.D Candidate - Materials Science 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] Water models and diffusion coefficient
Hello, For the record there are Water Models using effective pair potentials: J. Chem. Phys. 114, 6720 (2001) http://dx.doi.org/10.1063/1.1356002 Best, -m On 9 February 2013 14:45, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-02-09 14:21, Joinforfun Doe wrote: Hello, I am simulating a model of heavy water, with charges modified from SPCE model. This was proposed by Grigera [2001], with H replaced by D and charges on O and H increased from values proposed in SPCE model. I have verified by using gmxdump that gromacs sees the mass of H as 2.014 amu and the charges as specified in the topology file. The density comes out as expected for heavy water. The system equilibrates well (well-defined fluctutations, no trends in energy, density, pressure, temperature) However, the diffusion coefficient is always lower than that expected for the model. By using the same parameter files I ran a simulation for normal water (SPCE) model and the diffusion coefficient matches with that reported from other simulations. Is there something else that I should check? or is there something about g_msd that I am missing? Any pointers would be really helpful. Thanks Most water models have too high D. (see J Chem Phys 108 pp. 10220-10230 (1998)). SPC/E is about right. However that is more luck than skill so to speak, since there still is a lot of physics missing from this extremely simple model. So if you can reproduce literature values for the model and some experimental data, dens, DHvap, then this is as good as it gets. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.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 -- 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] Reference structure for PCA.
Hi vivek, I have few questions related to your query: During covariance matrix calculation, g_covar by default takes average structure of the trajectory as a reference structure then why you are giving it average structure of your trajectory (0-100ns) manually. Moreover without looking at your commands which you have used, it would be difficult for anyone that why are you getting these surprising results. On Thu, Feb 7, 2013 at 1:26 PM, vivek modi modi.vivek2...@gmail.com wrote: Hello, I have troubled you with a similar question before also, but I guess I need some more clarification. My question is about the reference structure in PCA analysis. I have 100ns long protein simulation which I want to analyze using PCA. The RMSD shows fluctuations upto initial 25-30ns and then becomes very stable. I have performed PCA on the last 30ns window of the simulation where I assume the simulation has converged (I also did on other time windows as well). The question is this: I did the analysis on the last 30ns window in two ways by taking two different reference structures. a. I take the average structure of the trajectory (0-100ns) as the reference and then do the fitting and calculate covariance matrix for last 30ns. This is done because I suspect that the average structure over full trajectory will reflect all the changes occurring in the protein. It also gives me low cosines (0.1). The PCs show movement occurring in certain regions of the protein. b. I take the average structure from the same window (last 30ns) then do the fitting and calculate covariance matrix for the same. This is done with an assumption that the reference structure must reflect the equilibriated/stable part of the trajectory unlike the previous case. Surprisingly it gives me high cosines (0.5). Unlike the previous case, this method shows very small movement in the protein (very low RMSF). Both of these methods give me different RMSF for the PCs although they are done on the same part of the trajectory but the reference structure is influencing the output. Which protocol among the two is appropriate ? And how can we explain high cosines in second case where the reference structure is the average of the same time window (there must not be large deviation) while I get low cosine for the first case where deviations are calculated from the full trajectory average (large deviation) ? Any help is appreciated. Thanks, -Vivek Modi Graduate Student IITK. -- 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 -- *--- Thanks and Regards, Bipin Singh* -- 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] Re: Water models and diffusion coefficient
For a simulation that is 300 ns long (after NVT and NPT equilibration steps of 1 ns each), I am saving output every 2 ps. The time step is 2 fs. nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps Is that saving data too rarely? Thanks, -- View this message in context: http://gromacs.5086.n6.nabble.com/Water-models-and-diffusion-coefficient-tp5005377p5005385.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Water models and diffusion coefficient
On 2013-02-09 19:26, learnmd wrote: For a simulation that is 300 ns long (after NVT and NPT equilibration steps of 1 ns each), I am saving output every 2 ps. The time step is 2 fs. nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps Is that saving data too rarely? No but check the flags in g_msd. Try without restarting, that is -trestart 31. Thanks, -- View this message in context: http://gromacs.5086.n6.nabble.com/Water-models-and-diffusion-coefficient-tp5005377p5005385.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.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] Reference structure for PCA.
Hi, The commands would certainly help, including the commands for getting the reference structure. Do note that the reference is the reference for fitting, which is 'external', i.e. provided by the user. This is not the same as the structure used to calculate the deviations, which is the average structure of the frames selected. Cheers, Tsjerk On Sat, Feb 9, 2013 at 7:06 PM, bipin singh bipinel...@gmail.com wrote: Hi vivek, I have few questions related to your query: During covariance matrix calculation, g_covar by default takes average structure of the trajectory as a reference structure then why you are giving it average structure of your trajectory (0-100ns) manually. Moreover without looking at your commands which you have used, it would be difficult for anyone that why are you getting these surprising results. On Thu, Feb 7, 2013 at 1:26 PM, vivek modi modi.vivek2...@gmail.com wrote: Hello, I have troubled you with a similar question before also, but I guess I need some more clarification. My question is about the reference structure in PCA analysis. I have 100ns long protein simulation which I want to analyze using PCA. The RMSD shows fluctuations upto initial 25-30ns and then becomes very stable. I have performed PCA on the last 30ns window of the simulation where I assume the simulation has converged (I also did on other time windows as well). The question is this: I did the analysis on the last 30ns window in two ways by taking two different reference structures. a. I take the average structure of the trajectory (0-100ns) as the reference and then do the fitting and calculate covariance matrix for last 30ns. This is done because I suspect that the average structure over full trajectory will reflect all the changes occurring in the protein. It also gives me low cosines (0.1). The PCs show movement occurring in certain regions of the protein. b. I take the average structure from the same window (last 30ns) then do the fitting and calculate covariance matrix for the same. This is done with an assumption that the reference structure must reflect the equilibriated/stable part of the trajectory unlike the previous case. Surprisingly it gives me high cosines (0.5). Unlike the previous case, this method shows very small movement in the protein (very low RMSF). Both of these methods give me different RMSF for the PCs although they are done on the same part of the trajectory but the reference structure is influencing the output. Which protocol among the two is appropriate ? And how can we explain high cosines in second case where the reference structure is the average of the same time window (there must not be large deviation) while I get low cosine for the first case where deviations are calculated from the full trajectory average (large deviation) ? Any help is appreciated. Thanks, -Vivek Modi Graduate Student IITK. -- 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 -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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: question about fftw3 in gromacs 4.6 installation
Hi guys!
Thanks for help!
I have finally manage to solve this problem.
Like Szilárd notice it was a problem with assembler.
When I installed binutils-2.23.1 (previously I had 2.20.1) it worked :)
So my combination was gcc 4.7.2 and binutils-2.23.1.
All the best!
tomek
On Sun, Feb 3, 2013 at 12:14 AM, Christoph Junghans jungh...@votca.orgwrote:
Date: Fri, 01 Feb 2013 19:00:02 -0500
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Re: question about fftw3 in gromacs 4.6
installation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 510c5702.5080...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2/1/13 5:26 PM, didymos wrote:
Hi Justin!
I had the same problem and I used your advise but I am not sure if this
entirely worked for me...
I used:
cmake -DGMX_MPI=ON DCMAKE_INSTALL_PREFIX=$HOME/gromacs
-DFFTWF_INCLUDE_DIR=$HOME/fftw/include
-DFFTWF_LIBRARY=$HOME/fftw/lib/libfftw3f.so
-DCMAKE_PREFIX_PATH=$HOME/fftw/
..
The use of -DCMAKE_PREFIX_PATH eliminates the need for
-DFFTWF_INCLUDE_DIR and
-DFFTWF_LIBRARY. Not that this is the source of your problem, but you
can
certainly trim down your command.
and I got:
-- checking for module 'fftw3f'
-- found fftw3f, version 3.2.2
-- Looking for fftwf_plan_r2r_1d in
/home/users/didymos/fftw/lib/libfftw3f.so
-- Looking for fftwf_plan_r2r_1d in
/home/users/didymos/fftw/lib/libfftw3f.so - found
-- Looking for fftwf_have_simd_avx in
/home/users/didymos/fftw/lib/libfftw3f.so
-- Looking for fftwf_have_simd_avx in
/home/users/didymos/fftw/lib/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in
/home/users/didymos/fftw/lib/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in
/home/users/didymos/fftw/lib/libfftw3f.so - found
So it seems ok but I am not sure about first two lines:
-- checking for module 'fftw3f'
-- found fftw3f, version 3.2.2
it should be 3.3.3
Is there a different FFTW installed anywhere else on your system? I
believe the
first found fftw3f statement comes from pkgconfig detection, but this
is
superseded by what you specify manually. Perhaps someone who is more
familiar
with this element of the build system can comment.
Justin is 100% right, -DFFTWF_{INCLUDE_DIR,LIBRARY} supersedes,
whatever pkg-config finds before, you can see which library is used in
the output, in your case /home/users/didymos/fftw/lib/libfftw3f.so is
used.
One can also tweak the pkg-config's detection by including
/home/users/didymos/fftw in its search path:
export PKG_CONFIG_PATH=$HOME/fftw/lib/pkgconfig
and test if it works by
$ pkg-config --libs fftw3f
(I should add this trick to the wiki as setting PKG_CONFIG_PATH helps
to tweak the detection of fftw and gsl (when installed in same custom
location) with one variable.)
Christoph
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
Christoph Junghans
Web: http://www.compphys.de
--
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Re: [gmx-users] Questions about parameters in topology file
On 2/9/13 3:14 AM, Ali Alizadeh wrote: Dear All user I am using oplsa.ff( in forcefield.itp : oplsa use combination rule 3 , A part of my topology file, Can I use my parameters instead of force filed parameters in my topology file?, for example: You can do whatever you like to modify the parameters, just make sure they don't completely break the force field ;) -Justin A part of my topology file, - . . . . [ pairs ] ; aiaj funct V(sigma) W(e) 1 4 1 0.3905 0.7330109793 1 9 1 0.3905 0.6017887953 2 5 1 0.3905 0.7330109793 210 1 0.3905 0.7330109793 3 6 1 0.3905 0.7330109793 3 8 1 0.3905 0.7330109793 4 7 1 0.3905 0.6017887953 9 7 1 0.3905 0.494012928 -- -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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] Removing errors related to missing dihedrals.
Dear Gromacs Users. I generated a topology file of GDP for OPLSAA force field using MKTOP. But on running grompp I got a list of No default Angle types and No default Ryckaert Bell. types error. So this time i manually assigned the appropriate atom types by looking up the atomtypes.atp file and managed to come down from 24 errors to 9 errors. All the errors correspond to missing dihedrals only. I notice that these missing dihedrals are concentrated around two specific region of the structures which are the Pyramidine ring of Guanine and the bond connecting the C1 atom of ribose and N9 atom of the imidazole ring of Guanine. So i have a two part query: 1. I had assigned the atom types for the Guanine part of GDP from the already defined atom types for Guanine in the library. Is it not then surprising to get 6 missing dihedrals for the pyramidine ring considering the fact that Guanine is already parameterized ? Am i wrong in this ? 2. In an effort to remove the missing dihedral errors related to the C1-N9 region it tried to manually add the missing diherals to the ffbonded.itp file. I noticed one of the missing dihedral was: OH-CT-CT-NA (O2'-C2'-C1'-N9). So i added the dihedral entry as: NA CT CT OH 3 16.73600 -16.73600 0.0 0.0 0.0 0.0 based on an already defined dihedral: NT CT CT OH 3 16.73600 -16.73600 0.0 0.0 0.0 0.0. But the error corresponding to this dihedral remained on re-run. Is there anything wrong with this ? Do i need to edit some other related files. I am very new to gromacs. Kindly help as I'm stuck. Thanks in advance. Abhishek Acharya M.Tech Structural Biology Lab Biological Sciences and Bioengineering Department Indian Institute of Technology Kanpur. -- 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
