Re: [gmx-users] error after grompp
Hello, Hi all, I need to do simulation which same as protein-ligand tutorial by Justin. The different is i'm using my protein and the ligand was zinc. I already follow everything in that tutorial and suddenly when i want to heat my protein by using the nvt.mdp there was an error state like below : Fatal error: Atom 410 in multiple T-Coupling groups (1 and 2) This means that atom no. 410 is defined in both the coupling groups which you have defined in the temperature coupling segment of your mdp file. Looking at your file it seems to me that the Zn atom is the culprit. In case the parameters for the Zn are being directly taken from the force field ions.itp file, then i think gromacs treats this as an ion and would automatically assigns to Water_and _ions group. Actually I do not understand what the error said even when i'm Google it to forum there was no one facing like mine..Here i put together my topology and the nvt.mdp. Hope you can give me some idea that i cant see. Another question,why is in the nvt.mdp at the temperature coupling there were twice of 300 of tcoupl and also the tau_t : 01. 01. Can u explain it why? this has been explained quite clearly in the gromacs manual. In essence, defining different coupling groups allows control over the temperature of the Groups especially protein and water which otherwise have been seen to differ in the temperature attained by a large degree. Cheers Abhishek Acharya Structural and Computational Biology Lab IIt 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
[gmx-users] Re: REMD analysis
Dear gmx members, I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 steps. The output of md.log file is : Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 Repl .16 .16 .16 .17 .18 .21 .24 .26 .28 .30 Repl number of exchanges: Repl 0123456789 10 Repl 2038 2007 2065 2117 2182 2587 3022 3213 3554 3703 Repl average number of exchanges: Repl 0123456789 10 Repl .16 .16 .17 .17 .17 .21 .24 .26 .28 .30 The acceptance ratio for each replica and average acceptance ratio is as calculated below :- accp. ratio 2038 0.16304 2007 0.16056 2065 0.1652 2117 0.16936 2182 0.17456 2587 0.20696 3022 0.24176 3213 0.25704 3554 0.28432 3703 0.29624 0.211904 (avg accp ratio) The Pdes used while generating temp. range was also 0.2. Does that mean that replicas have exchanged for the given temp.range ??. Here's the link for both remd_temp and remd_index files ( https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png) , ( https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m) -- Bharat -- 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
Aw: Re: [gmx-users] PCA_RMS fluctuation per residue?
You should make a good index file and read the options in g_covar and g_anaeig in the manual and just the command line help. I found the new builds of Gromacs allows indexing after a long trajectory, but did not know this before hand. I had tried it with older versions, a couple years back, but it complained about wrong index groups set...so dont know if it was a fix or somthin else on my side from older to newer versions. Gesendet:Mittwoch, 08. Mai 2013 um 08:25 Uhr Von:Tsjerk Wassenaar tsje...@gmail.com An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] PCA_RMS fluctuation per residue? Hi Rajiv, Square the values, sum them per residue and take the square root. Cheers, Tsjerk On May 8, 2013 7:24 AM, ra...@kaist.ac.kr wrote: Dear gmx users, Ive done covariance matrix for backbone of protein using g_covar command. Also, can able to plot all projections through g_anaeig. However, I could only able to do -rmsf: plot the RMS fluctuation per atom of eigenvectors BUT i wants to do them per residue? How can i achieve this? In manual it shows -filt: command filter the trajectory to show only the motion along eigenvectors. How i do visualize this kind of motions? Rajiv -- gmx-users mailing list gmx-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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant 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] issue in replica exchange
I finally could reproduce the problem in gmx461 and have fled up a red mine report. I hope we can fix this easily but I am not sure how things go go from now! Someone will get the bug assigned and fix it when ever possible or something else? Thank you all for the help, XAvier. On May 2, 2013, at 10:15 PM, XAvier Periole x.peri...@rug.nl wrote: I'll look at the 4.6.1 version next week, I could install it but I got a conflict between the environmental variable defining openMP variable but I turned it off during compilation … You could try to run on particle decomposition to see if you get a problem … it should one quite quick. On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote: Both. So if 4.6.1 doesn't work, I want to know so we can patch it before 4.6.2 comes out. If it does work, then there is probably stuff that can be backported. On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote: You mean working with or working on the code? I'll try gmx-4.6.1 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote: Quick check here -- is 4.6 behaving correctly? I actually spent some time working on REMD in 4.6, and it seems to be behaving correctly in my hands with temperature and pressure control. Thanks for any additional info on this! On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote: I saw that redmine report, which could be related but it seems to happen only for runs done outside the domain and particle decompositions. I'll fill up a red mine. Anything I could do to help speeding the fix? What'd be really nice is some thought on how one can demonstrate that the implementation of the exchange matches what would be expected from the theory. For T-exchange under NVT, it is sufficient to rescale velocities and quantities derived from them by the correct factor. That includes various things like T-coupling history and integrator half-step quantities (and does REMD with leap-frog make sense anyway?). For NPT, there's probably also some P-coupling quantities to scale, and the box to exchange. Anything I've missed? Hopefully virial contributions don't matter either way? Perhaps a decent first step is to hack the code to do a self exchange, by clearing the entire state and rebuilding with what would/should be received from an exchange with a hypothethetical replica in an identical pre-exchange state. Only if the code can do that (i.e. mdrun -reprod produces a trajectory indistinguishable from a run that does not attempt this self exchange) is it worth considering proper state exchanges, and the process of making the code do the former should illustrate what is required for the latter. 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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
[gmx-users] trjcat: joining randomized PDB files
Dear ALL, I want to randomize the frames of my trajectory for calculating convergence. For this, I have dropped the frames as PDB files using trjconv and then renamed them randomly. Now I want to join these randomized PDB frames to get a randomized trajectory using trajcat. But somehow trjcat always joins them in proper frame order (inspite of completely random PDB file names). How can I join the randomly to get a randomized trajectory? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] trjcat: joining randomized PDB files
On 5/9/13 9:35 AM, Anirban wrote: Dear ALL, I want to randomize the frames of my trajectory for calculating convergence. For this, I have dropped the frames as PDB files using trjconv and then renamed them randomly. Now I want to join these randomized PDB frames to get a randomized trajectory using trajcat. But somehow trjcat always joins them in proper frame order (inspite of completely random PDB file names). How can I join the randomly to get a randomized trajectory? Any suggestion is welcome. Use -settime and give them arbitrary time values. -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 -- 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] trjcat: joining randomized PDB files
Thanks a lot Justin, for the reply. But with -settime for every file I have to interactively give arbitrary values. I have around 500 PDB files for one part of the trajectory and there are total 10 parts. So its very difficult to repeat this for around 5000 times. Is there any other option. trjcat reads the randomized PDB files serially, so can't it just concatenate the files in that order? Or am I missing something? Thanks again. Regards, Anirban On Thu, May 9, 2013 at 7:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/9/13 9:35 AM, Anirban wrote: Dear ALL, I want to randomize the frames of my trajectory for calculating convergence. For this, I have dropped the frames as PDB files using trjconv and then renamed them randomly. Now I want to join these randomized PDB frames to get a randomized trajectory using trajcat. But somehow trjcat always joins them in proper frame order (inspite of completely random PDB file names). How can I join the randomly to get a randomized trajectory? Any suggestion is welcome. Use -settime and give them arbitrary time values. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fw: probability from COM of micelle
Dear GROMACS Specialist, I want to plot probability (nm^-1) distribution of micelle selected atoms with respect to COM of the micelle (nm). with respect to this definition, Probability was defined as the number of instances the selected atom was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM divided by r, may I ask you to give me one formula to plot of this probability, Please? for example, to plot of density(nm^-3) with respect to COM of micelle (nm), I do as following: density = g(r) * (N/V) Thank you very much in advance. 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] Re: A problem with do_dssp command
OK, thank you very much. -- View this message in context: http://gromacs.5086.x6.nabble.com/A-problem-with-do-dssp-command-tp5008049p5008089.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] trjcat: joining randomized PDB files
On 5/9/13 9:50 AM, Anirban wrote: Thanks a lot Justin, for the reply. But with -settime for every file I have to interactively give arbitrary values. I have around 500 PDB files for one part of the trajectory and there are total 10 parts. So its very difficult to repeat this for around 5000 times. Is there any other option. trjcat reads the randomized PDB files serially, so can't it just concatenate the files in that order? Or am I missing something? Interactive prompts like this are easy to use in scripts. http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts I have never tried with trjcat, but it seems to me that you can easily loop through any arbitrary set of numbers stored in a variable as the time value to be passed to trjcat. -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 -- 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] Fw: probability from COM of micelle
On 5/9/13 10:15 AM, mohammad agha wrote: Dear GROMACS Specialist, I want to plot probability (nm^-1) distribution of micelle selected atoms with respect to COM of the micelle (nm). with respect to this definition, Probability was defined as the number of instances the selected atom was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM divided by r, may I ask you to give me one formula to plot of this probability, Please? for example, to plot of density(nm^-3) with respect to COM of micelle (nm), I do as following: density = g(r) * (N/V) It sounds like all you need to do is create a histogram from data produced by g_dist. You can make the histogram with g_analyze or any number of other programs. -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 -- 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] Fw: probability from COM of micelle
On 2013-05-09 20:15, Justin Lemkul wrote: On 5/9/13 10:15 AM, mohammad agha wrote: Dear GROMACS Specialist, I want to plot probability (nm^-1) distribution of micelle selected atoms with respect to COM of the micelle (nm). with respect to this definition, Probability was defined as the number of instances the selected atom was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM divided by r, may I ask you to give me one formula to plot of this probability, Please? for example, to plot of density(nm^-3) with respect to COM of micelle (nm), I do as following: density = g(r) * (N/V) It sounds like all you need to do is create a histogram from data produced by g_dist. You can make the histogram with g_analyze or any number of other programs. -Justin How about g_rdf? -- 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] Charmm27 potential energies.
Hello, I am attempting to generate force-field parameters for a fatty acid molecule that contains a carboxilic acid head group. I decided to use the parameters for stearic acid as the base for my molecule, since they contain similar structures with the only major change being a shorter hydrophobic tail. I noticed that the charge on stearic acid, and other molecules that have a carboxilic head group, is spread out with -0.9 residing on the head group and -0.1 on the second carbon. I need to use the protonated from of my molecule for my simulation, as well as the deprotonated form. I looked into the parameters for the COOH replacement in the Charmm27 force-field and used that to form the head group of the protonated form of my molecule. The problem that I am facing is that this left behind a charge of -0.1 that resides on the second carbon. Is there any way to find acceptable partial charges without doing the full Gaussian calculations? I would also appreciate it if someone could explain why the charges were split onto the second carbon in the first place. Thanks in advance, Eric Stokes -- 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] Charmm27 potential energies.
On 5/9/13 4:33 PM, Eric Stokes wrote: Hello, I am attempting to generate force-field parameters for a fatty acid molecule that contains a carboxilic acid head group. I decided to use the parameters for stearic acid as the base for my molecule, since they contain similar structures with the only major change being a shorter hydrophobic tail. I noticed that the charge on stearic acid, and other molecules that have a carboxilic head group, is spread out with -0.9 residing on the head group and -0.1 on the second carbon. I need to use the protonated from of my molecule for my simulation, as well as the deprotonated form. I looked into the parameters for the COOH replacement in the Charmm27 force-field and used that to form the head group of the protonated form of my molecule. The problem that I am facing is that this left behind a charge of -0.1 that resides on the second carbon. Is there any way to find acceptable partial charges without doing the full Gaussian calculations? I would also appreciate it if someone could explain why the charges were split onto the second carbon in the first place. Servers exist for this purpose, like SwissParam and ParamChem. As for the charge assignments, you would have to investigate the primary literature source for those parameters and how they were fitted. -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 -- 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] groups selection make_ndx -f npt.gro
Hello sir As in the tutorial for umbrella sampling command make_ndx -f npt.gro you have selected two different groups as Chain_A as 19 and Chain_B as 20 If we have protein-ligand interaction whether we should have single group of protein-ligand complex or we should use two different groups for protein and ligand. Regards Arunima -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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] probability from COM of micelle
Dear GROMACS Specialists, Thank you very much from your answer, but I want to know plotting this curve from g_rdf. May I ask you to give me one formula by this command, Please? Best Regards Sara On 2013-05-09 20:15, Justin Lemkul wrote: On 5/9/13 10:15 AM, mohammad agha wrote: Dear GROMACS Specialist, I want to plot probability (nm^-1) distribution of micelle selected atoms with respect to COM of the micelle (nm). with respect to this definition, Probability was defined as the number of instances the selected atom was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM divided by r, may I ask you to give me one formula to plot of this probability, Please? for example, to plot of density(nm^-3) with respect to COM of micelle (nm), I do as following: density = g(r) * (N/V) It sounds like all you need to do is create a histogram from data produced by g_dist. You can make the histogram with g_analyze or any number of other programs. -Justin How about g_rdf? -- 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.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-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] Charmm27 potential energies.
The positive charge on the alpha-carbon should be expected. Many methods (not only DFT) will predict tiny non-zero charges even on more remote carbons, if you consider deprotonated form. Protonated form is a neutral molecule. So, alpha -CH2- may be acceptably described as having a a zero charge in total. You can distribute the +1e charge throughout COOH (for instance, uniformly with respect to what you have in COO(-)) to make it also neutral in total. On a related note, it is not very time consuming to calculate electronic structures of CH3-COOH(0e) and CH3-COO(-1e) and derive better electrostatic charges for each site. Dr. Vitaly Chaban On Thu, May 9, 2013 at 11:33 PM, Eric Stokes es...@uw.edu wrote: Hello, I am attempting to generate force-field parameters for a fatty acid molecule that contains a carboxilic acid head group. I decided to use the parameters for stearic acid as the base for my molecule, since they contain similar structures with the only major change being a shorter hydrophobic tail. I noticed that the charge on stearic acid, and other molecules that have a carboxilic head group, is spread out with -0.9 residing on the head group and -0.1 on the second carbon. I need to use the protonated from of my molecule for my simulation, as well as the deprotonated form. I looked into the parameters for the COOH replacement in the Charmm27 force-field and used that to form the head group of the protonated form of my molecule. The problem that I am facing is that this left behind a charge of -0.1 that resides on the second carbon. Is there any way to find acceptable partial charges without doing the full Gaussian calculations? I would also appreciate it if someone could explain why the charges were split onto the second carbon in the first place. Thanks in advance, Eric Stokes -- 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] US and SMD
Hi, In Umbrella Sampling method, among mdp settings, there is a section where the pull code settings are defined in: pull = umbrella: using a harmonic potential to pull As it is said that with US the path of the permeating ion along thereaction coordinate is sampled using many discrete windows, whereas with SMD the ion is pulledalong this same reaction coordinate, I am on a doubt that how the pull code with a harmonic potential works here? I am little confused. Would you please giveme a hint to understand it? Thanks in advance. Your suggestionswould be appreciated . Sincerely, Shima -- 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
