Re: [gmx-users] citation for pdb2gmx -vsite hydrogens
That's the one. 7 maj 2012 kl. 22.34 skrev Christopher Neale: Dear users: I am writing my methods section for a simulation in which I used -vsites hydrogens and I want to ensure that I have the reference correct. The gmx-4.5.4 manual does not list a reference that I could see for this usage by searching vsites. Is this the correct reference: Feenstra, Hess, Berendsen, J. Comput. Chem. 1999, 20(8), pp786-798 http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(199906)20:8%3C786::AID-JCC5%3E3.0.CO;2-B/abstract Thank you, Chris. -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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: Justin lipid-position restraine
On Tue, May 8, 2012 at 1:00 PM, rama david ramadavidgr...@gmail.com wrote: Hi Gromacs user, I am doing the justin tutorial on lipid posted on link.. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I am following the tutorial very carefully ... As mentioned in the tutorial I need to generate strong position restrained on proteins heavy atoms to ensure that position of atom does not change during EM (Energy Minimisation ) My command line is as follow . genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Reading structure file Select group to position restrain Group 0 ( System) has 138 elements Group 1 (Protein) has 138 elements Group 2 ( Protein-H) has 109 elements Group 3 (C-alpha) has16 elements Group 4 ( Backbone) has48 elements Group 5 ( MainChain) has64 elements Group 6 ( MainChain+Cb) has78 elements Group 7 (MainChain+H) has81 elements Group 8 ( SideChain) has57 elements Group 9 (SideChain-H) has45 elements Select a group: I am using Gromacs 4.5.4 Generally position restrain is applied on backbone of protein So I choose backbone (4) Is it right or I have to choose the group protein(138 elements) to apply position restraine on all protein atoms All suggestions are welcome thank you in advance Rama David . -- 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] Getting local pressure
g_density 8 maj 2012 kl. 03.29 skrev cuong nguyen: Dear, Could anyone please let me know, in Gromacs analysis is there any way to get the local pressure (along z-axis of the box)? Thanks a lot! Cuong Nguyen -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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: Justin lipid-position restraine
On Tue, May 8, 2012 at 1:01 PM, rama david ramadavidgr...@gmail.com wrote: On Tue, May 8, 2012 at 1:00 PM, rama david ramadavidgr...@gmail.comwrote: Hi Gromacs user, I am doing the justin tutorial on lipid posted on link.. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html I am following the tutorial very carefully ... As mentioned in the tutorial I need to generate strong position restrained on proteins heavy atoms to ensure that position of atom does not change during EM (Energy Minimisation ) My command line is as follow . genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 Reading structure file Select group to position restrain Group 0 ( System) has 138 elements Group 1 (Protein) has 138 elements Group 2 ( Protein-H) has 109 elements Group 3 (C-alpha) has16 elements Group 4 ( Backbone) has48 elements Group 5 ( MainChain) has64 elements Group 6 ( MainChain+Cb) has78 elements Group 7 (MainChain+H) has81 elements Group 8 ( SideChain) has57 elements Group 9 (SideChain-H) has45 elements Select a group: I am using Gromacs 4.5.4 Generally position restrain is applied on backbone of protein So I choose backbone (4) Is it right or I have to choose the group protein(138 elements) to apply position restraine on all protein atoms As the tutorial suggest you can restrain the heavy atoms, but I usually restrain the entire protein during the InflateGro steps (EMs) and let the lipids minimize around it. -Anirban All suggestions are welcome thank you in advance Rama David . -- 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] Calculation of the components of (ionic) current using g_current
Hi, it is the ionic current, given by a sum over the center of mass velocities of each molecule by their net-charge. /Flo On Mon, 2012-05-07 at 13:00 -0400, Andrew DeYoung wrote: Hi, g_current calculates the (ionic) current in the output file specified by the -o switch (by default, current.xvg). Specifically, each component (x, y, and z) of the current is computed and printed. My question is, is the current that is computed the current of atoms (which each have partial charges), or is it the current of molecules (ionic molecules have non-zero charge, whereas neutral molecules have zero charge)? I am guessing that it is the former -- the current of atoms. However, I am not certain, because when I run g_current, part of the output says, for example: Split group of 6144 atoms into 512 molecules which seems to imply that the code uses the topology (I provide the code with a .tpr file) to determine the connectivity of atoms. Thanks so much! Andrew DeYoung Carnegie Mellon University -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] justin-lipid tutorial........
Hi gromac friends I am performing the justin tutorials on lipids http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials I am strugling now on 3rd steps I have following queris regarding to steps ... 1. I increase the van der walls radii of carbon from the 0.15 to 0.375 Is these also increases the vanderwall radii of protein ...?? If it increases the radii of protein , then how to add water in protein core ...??? 2. What is the meaning of continue to adjust the van der waals radius of carbon ??? Please comment in detail... 3. After solvation I given the following command to ion addition grompp -f ions.mdp -c solv.pdb -p topol.top -o ions.tpr I got following reply ... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 837 of the 2346 non-bonded parameter combinations --- Program grompp, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 479 Fatal error: No molecules were defined in the system For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Making merry out of nothing, like in refugee camp (Gogol Bordello) Please give me some valuable suggestion Rama David... With Best Wishes, -- 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] justin-lipid tutorial........
On 5/8/12 8:06 AM, rama david wrote: Hi gromac friends I am performing the justin tutorials on lipids http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials I am strugling now on 3rd steps I have following queris regarding to steps ... 1. I increase the van der walls radii of carbon from the 0.15 to 0.375 Is these also increases the vanderwall radii of protein ...?? If it increases the radii of protein , then how to add water in protein core ...??? It will affect all carbon atoms. If you need to do something more specialized, you'll probably have to use a different approach. The above suggestion is to eliminate water from being placed within the lipid membrane. 2. What is the meaning of continue to adjust the van der waals radius of carbon ??? Please comment in detail... Continue to adjust = change the value until you get satisfactory results. The value of 0.375 generally works well for me, but some lipids pack differently and thus you may need to use a different value. For the tutorial, which uses DPPC, 0.375 should work fine. 3. After solvation I given the following command to ion addition grompp -f ions.mdp -c solv.pdb -p topol.top -o ions.tpr I got following reply ... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 837 of the 2346 non-bonded parameter combinations --- Program grompp, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 479 Fatal error: No molecules were defined in the system For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Making merry out of nothing, like in refugee camp (Gogol Bordello) Somehow you've badly broken the topology. At this point, it's hard to say how. -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] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder
Hello, I assume that you mean pull_pbcatom0... Nothing changes when I set this to an atom index I am afraid. I saw that you had use pull_geometry=cylinder in your recent JACS paper. Would it be too much to ask to see those pull settings? I simply cannot get the molecule to stay at the desired z-position... Thanks! Hi, we had similar trouble some time ago, and we could solve it by using a good PBC atom. Make sure that your pbc_atom is in the very center of your membrane. Btw, using distance to compare with cylinder is a bad test, since it does something very different (the distance is the same at z=com-1 and z=com+1. I would use direction or position for your test. You can also use position/direction for the umbrella simulations, you'll probably get similar results to the geometry cylinder, but you'll also have to make sure your pbc_atom is fine. Cheers, Jochen -- 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] Formyl parameters
Dear gmx users, My .pdb input file has a formyl group which is not defined in CHARMM27 and CHARMM36. So I got its .itp file through swissparam. Now I want to use its parametrs. As I read in gromacs.org , I need to include this .itp in .top file. How does it come when I have not got any .top file yet? Anybody can suggest me how I can use .itp file and solve my problem? Thanks in advance, 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
Re: [gmx-users] Formyl parameters
On 5/8/12 11:25 AM, Shima Arasteh wrote: Dear gmx users, My .pdb input file has a formyl group which is not defined in CHARMM27 and CHARMM36. So I got its .itp file through swissparam. Now I want to use its parametrs. As I read in gromacs.org , I need to include this .itp in .top file. How does it come when I have not got any .top file yet? Anybody can suggest me how I can use .itp file and solve my problem? The solution to the problem depends on what you need to do. Your use of the term formyl group seems to imply that it is an adduct to some existing molecule, i.e. C(=O)H. If this is correct, then you need to do one of two things: 1. Add the formyl group as an entry in the relevant .rtp file (using the parameters contained in the .itp file) so it can be used as a building block on its own. 2. Incorporate the parameters into an existing residue that it is modifying, though if this is the case you should be parameterizing a new residue rather than a formyl moiety. If the formyl group is actually a standalone molecule, i.e. formaldehyde or formate, then the solution is certainly as simple as adding an #include statement to the .top file. The source of the .top also depends on what you're doing. It can be generated by pdb2gmx in the case of a macromolecule or it can be written by hand in a text editor in simple cases. In any event, if you need further help, you need to post considerably more information about what you're trying to achieve. I can probably guess a few more potential scenarios, but I'd rather not waste a lot of time ;) -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] restarting simulation after segmentation fault
Dear gmx users I am simulating a system involving carbon nanotube. I successfully completed the EM,NVT and NPT equilibration phase and then started to run production simulation(NVT ensemble) for 10 ns.However, after passing more than 50 steps(1 ns),I gave the segmentation error.I investigated log file but it did not contain any errors so I used tpbconv and mdrun to restart the simulation.I would be pleased if you could tell me whether restarting the simulation after segmentation fault is correct or not? Best regards-- 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] restarting simulation after segmentation fault
On 5/8/12 11:40 AM, Za Pour wrote: Dear gmx users I am simulating a system involving carbon nanotube. I successfully completed the EM,NVT and NPT equilibration phase and then started to run production simulation(NVT ensemble) for 10 ns.However, after passing more than 50 steps(1 ns),I gave the segmentation error.I investigated log file but it did not contain any errors so I used tpbconv and mdrun to restart the simulation.I would be pleased if you could tell me whether restarting the simulation after segmentation fault is correct or not? More often than not, a segmentation fault indicates the system is unstable and will likely crash again. The log file will not indicate any errors, but information printed to stderr/stdout will. -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] radius of gyration
Dear GROMACS Specialists, I have one question about radius of gyration for micelle, Please help me. My micelle is created at 10 ps by Martini CG force field. When I calculate the radius of gyration from this time as g_gyrate -f 1.xtc -s 1.tpr -n 1.ndx -o gyrate.xvg -b 10 and g_analyze -f gyrate.xvg -av -ee, my answer is: std. dev. relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 1.811581e+00 1.586248e-02 3.708049e-05 0.399 0.318 SS2 1.476027e+00 5.355297e-02 1.251867e-04 0.009 -0.039 SS3 1.480446e+00 5.226397e-02 1.221735e-04 0.004 -0.060 SS4 1.478287e+00 5.332558e-02 1.246551e-04 -0.005 -0.084 Set 1: err.est. 0.000281889 a 0.468124 tau1 20.1606 tau2 308.225 Set 2: err.est. 0.0024333 a 0.925872 tau1 536.208 tau2 8592.94 Set 3: err.est. 0.00190226 a 0.971916 tau1 544.756 tau2 7044.58 Set 4: err.est. 0.00267771 a 0.991392 tau1 629.613 tau2 88302 But when I calculate it from start time of simulation as g_gyrate -f 1.xtc -s 1.tpr -n 1.ndx -o gyrate.xvg and g_analyze -f gyrate.xvg -av -ee, my answer is: std. dev. relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 1.979407e+00 6.228274e-01 1.392685e-03 2.317 4.169 SS2 1.613785e+00 5.401095e-01 1.207722e-03 2.478 4.949 SS3 1.601265e+00 4.713569e-01 1.053986e-03 2.547 5.460 SS4 1.624623e+00 5.387790e-01 1.204746e-03 2.208 3.719 Warning: tau2 is longer than the length of the data (1.2e+06) the statistics might be bad invalid fit: e.e. -nan a 5.56656 tau1 674505 tau2 8.75077e+07 Will fix tau2 at the total time: 1.2e+06 a fitted parameter is negative invalid fit: e.e. -nan a 18.789 tau1 806548 tau2 1.2e+06 Will use a single exponential fit for set 1 Set 1: err.est. 0.212562 a 1 tau1 69885.8 tau2 0 a fitted parameter is negative invalid fit: e.e. 20.1017 a 2.22647 tau1 210523 tau2 -6.77257e+08 Will fix tau2 at the total time: 1.2e+06 a fitted parameter is negative invalid fit: e.e. -nan a 3.04296 tau1 249121 tau2 1.2e+06 Will use a single exponential fit for set 2 Set 2: err.est. 0.170009 a 1 tau1 59447.7 tau2 0 a fitted parameter is negative invalid fit: e.e. 0.139564 a 1.61177 tau1 36947.7 tau2 11359.6 Will fix tau2 at the total time: 1.2e+06 a fitted parameter is negative invalid fit: e.e. -nan a 2.35981 tau1 195092 tau2 1.2e+06 Will use a single exponential fit for set 3 Set 3: err.est. 0.149959 a 1 tau1 60729.6 tau2 0 a fitted parameter is negative invalid fit: e.e. 6.4854 a 5.92085 tau1 759910 tau2 -1.67528e+07 Will fix tau2 at the total time: 1.2e+06 a fitted parameter is negative invalid fit: e.e. -nan a 30.0389 tau1 922726 tau2 1.2e+06 Will use a single exponential fit for set 4 Set 4: err.est. 0.184771 a 1 tau1 70566.6 tau2 0 and my plot of errest.xvg in the first one is similar with article B. Hess, J. Chem. Phys. 116:209-217, 2002 but in the second one is different whereas err.est in second are similar to micellar articles. I don't know which one is true, time of simulation start or time of creation of micelle? Both of them (the radius of gyration) is in agreement with experimental but second one is more near than first one. 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] radius of gyration
On 5/8/12 1:06 PM, dina dusti wrote: Dear GROMACS Specialists, I have one question about radius of gyration for micelle, Please help me. My micelle is created at 10 ps by Martini CG force field. Does this mean that during the first 100 ns, there is no micelle? That is, it is only completely formed after 100 ns have passed? When I calculate the radius of gyration from this time as g_gyrate -f 1.xtc -s 1.tpr -n 1.ndx -o gyrate.xvg -b 10 and g_analyze -f gyrate.xvg -av -ee, my answer is: std. dev. relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 1.811581e+00 1.586248e-02 3.708049e-05 0.399 0.318 SS2 1.476027e+00 5.355297e-02 1.251867e-04 0.009 -0.039 SS3 1.480446e+00 5.226397e-02 1.221735e-04 0.004 -0.060 SS4 1.478287e+00 5.332558e-02 1.246551e-04 -0.005 -0.084 Set 1: err.est. 0.000281889 a 0.468124 tau1 20.1606 tau2 308.225 Set 2: err.est. 0.0024333 a 0.925872 tau1 536.208 tau2 8592.94 Set 3: err.est. 0.00190226 a 0.971916 tau1 544.756 tau2 7044.58 Set 4: err.est. 0.00267771 a 0.991392 tau1 629.613 tau2 88302 But when I calculate it from start time of simulation as g_gyrate -f 1.xtc -s 1.tpr -n 1.ndx -o gyrate.xvg and g_analyze -f gyrate.xvg -av -ee, my answer is: std. dev. relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 1.979407e+00 6.228274e-01 1.392685e-03 2.317 4.169 SS2 1.613785e+00 5.401095e-01 1.207722e-03 2.478 4.949 SS3 1.601265e+00 4.713569e-01 1.053986e-03 2.547 5.460 SS4 1.624623e+00 5.387790e-01 1.204746e-03 2.208 3.719 Warning: tau2 is longer than the length of the data (1.2e+06) the statistics might be bad invalid fit: e.e. -nan a 5.56656 tau1 674505 tau2 8.75077e+07 Will fix tau2 at the total time: 1.2e+06 a fitted parameter is negative invalid fit: e.e. -nan a 18.789 tau1 806548 tau2 1.2e+06 Will use a single exponential fit for set 1 Set 1: err.est. 0.212562 a 1 tau1 69885.8 tau2 0 a fitted parameter is negative invalid fit: e.e. 20.1017 a 2.22647 tau1 210523 tau2 -6.77257e+08 Will fix tau2 at the total time: 1.2e+06 a fitted parameter is negative invalid fit: e.e. -nan a 3.04296 tau1 249121 tau2 1.2e+06 Will use a single exponential fit for set 2 Set 2: err.est. 0.170009 a 1 tau1 59447.7 tau2 0 a fitted parameter is negative invalid fit: e.e. 0.139564 a 1.61177 tau1 36947.7 tau2 11359.6 Will fix tau2 at the total time: 1.2e+06 a fitted parameter is negative invalid fit: e.e. -nan a 2.35981 tau1 195092 tau2 1.2e+06 Will use a single exponential fit for set 3 Set 3: err.est. 0.149959 a 1 tau1 60729.6 tau2 0 a fitted parameter is negative invalid fit: e.e. 6.4854 a 5.92085 tau1 759910 tau2 -1.67528e+07 Will fix tau2 at the total time: 1.2e+06 a fitted parameter is negative invalid fit: e.e. -nan a 30.0389 tau1 922726 tau2 1.2e+06 Will use a single exponential fit for set 4 Set 4: err.est. 0.184771 a 1 tau1 70566.6 tau2 0 and my plot of errest.xvg in the first one is similar with article B. Hess, J. Chem. Phys. 116:209-217, 2002 but in the second one is different whereas err.est in second are similar to micellar articles. I don't know which one is true, time of simulation start or time of creation of micelle? Both of them (the radius of gyration) is in agreement with experimental but second one is more near than first one. If I am interpreting your situation correctly (and please do answer the question posed above), then the second case (which leads to an unreliable error estimate) incorporates 100 ns of time in which no micelle exists, so you're measuring something that you shouldn't, as it includes a substantial amount of time in which diffuse molecules will artificially increase the value of Rg if they are spread throughout the solvent. If after 100 ns, a micelle exists, then the first command is appropriate to measure its radius of gyration. -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] Wild-card atomt types - regd
Dear Gromacs users, I am planing to use wildcard atomtypes in [ dihedrals ] directive of the ffbonded.itp file, As my system contain O-C dihedral, all the O-C dihedrals are same, so instead of mentioning each dihedral explicitly i have tried wildcard atom types by specifing X-O-C-X but couldn't succeed,It is giving the error: No default Proper Dih. types. Is there any specific method to use wildcard atom types in Gromacs for dihedrals or do I have to define the wildcard atomtypes, if so in which file do i have to define it. Any help will be highly appreciated. Thank you in advance. Best regards, Ramesh cheerla -- 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] Wild-card atomt types - regd
On 5/8/12 1:44 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to use wildcard atomtypes in [ dihedrals ] directive of the ffbonded.itp file, As my system contain O-C dihedral, all the O-C dihedrals are same, so instead of mentioning each dihedral explicitly i have tried wildcard atom types by specifing X-O-C-X but couldn't succeed,It is giving the error: No default Proper Dih. types. Is there any specific method to use wildcard atom types in Gromacs for dihedrals or do I have to define the wildcard atomtypes, if so in which file do i have to define it. Wildcard entries are not specified in [dihedrals] directives, which are part of the .top; instead they are used in defining the parameters in the [dihedraltypes] directive of the ffbonded.itp file. That way, the dihedrals used in the .top are read from ffbonded.itp. -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] (no subject)
Dear Justin I really appreciate for your reply. -- 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] Charge derrivation for OPLSAA forcefield
Hi Guys I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP based charges for some molecules that I study. Is this a correct method to do so if not please let me know what are the other methods that are available. thanks alot Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA-- 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] (no subject)
Hi Guys I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP based charges for some molecules that I study using OPLSAA force field. Is this a correct method to do so if not please let me know what are the other methods that are available. thanks alot Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA-- 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] Slow-growth method question
Hello community, I recently ran several simulations using the g_bar method on several molecule decouplings and I even applied it to some functional group mutations and it seems to work out quite well so far. The only thing is that it requires several simulations to run. I'm attempting to replicate this group mutation using the original slow-growth method that others have done in the past just to see how well it compares to the g_bar method. I can't seem to find any sort of instructions on running this method on Gromacs.I have the parameters from g_bar below but I'm trying to figure out how to alternate them below for the slow growth method. Is it simply the delta_lambda parameter that needs to be changed? Would I have to divide the timesteps by delta_lambda to make sure it goes up to Lambda=1? How do you calculate the end result?Thank you. ; Free energy control stuff free_energy = yes ;*** - Indicates we are doing a free energy calculation, and that interpolation between the A and B states of the chosen molecule (defined below) will occur. init_lambda = 0.0 ;*** - Value of λ delta_lambda= 0 ;*** - The value of λ can be incremented by some amount per timestep (i.e., δλ/δt) in a technique called slow growth. This method can have significant errors associated with it, and thus we will make no time-dependent changes to our λ values. foreign_lambda = 0.05 ;*** - Additional values of λ for which ΔH will be written to dhdl.xvg (with frequency nstdhdl). The configurations generated in the trajectory at λ = init_lambda will have ΔH calculated for these same configurations at all values of λ = foreign_lambda. sc-alpha= 0.5 ;*** - the soft-core parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions sc-power= 1.0 ;*** - the power for lambda in the soft-core function, only the values 1 and 2 are supported sc-sigma= 0.3 ;*** - the soft-core sigma for particles which have a C6 or C12 parameter equal to zero or a sigma smaller than sc_sigma ;couple-moltype = SIM ;*** - name of moleculetype to decouple ;couple-lambda0 = vdw ;*** - all interactions are on at lambda=0 ;couple-lambda1 = none ;*** - only vdw interactions are on at lambda=1 couple-intramol = no ;*** - Do not decouple intramolecular interactions. That is, the λ factor is applied to only solute-solvent nonbonded interactions and not solute-solute nonbonded interactions. nstdhdl = 10 ;*** - The frequency with which ∂H/∂λ and ΔH are written to dhdl.xvg. A value of 100 would probably suffice, since the resulting values will be highly correlated and the files will get very large. You may wish to increase this value to 100 for your own work. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering -- 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] radius of gyration
Dear Justin, Thank you very much from your help. Yes, the micelle was created after 100 ns from start of simulation. If the first procedure is true, so why the error estimate is so small and why the error estimate of Rg is so different with Rg(x,y,z)? Please help me. 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] radius of gyration
On 5/8/12 4:08 PM, dina dusti wrote: Dear Justin, Thank you very much from your help. Yes, the micelle was created after 100 ns from start of simulation. If the first procedure is true, so why the error estimate is so small and why the error estimate of Rg is so different with Rg(x,y,z)? For the algorithmic specifics of how the error estimate is calculated, refer to Berk's paper. The error estimate is smaller in the case of starting after 100 ns because in the case where you consider all the data, you are calculating Rg of diffuse molecules and a micelle. You're considering two different states and thus your data are poorly converged with respect to that measurement. -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] radius of gyration
Dear Justin, Thank you very much from your help, but may I ask you to say me why the error estimate of Rg is very smaller than Rgx, Rgy, Rgz, Please? I didn't understand any thing from paper about this problem! Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 9, 2012 12:44 AM Subject: Re: [gmx-users] radius of gyration On 5/8/12 4:08 PM, dina dusti wrote: Dear Justin, Thank you very much from your help. Yes, the micelle was created after 100 ns from start of simulation. If the first procedure is true, so why the error estimate is so small and why the error estimate of Rg is so different with Rg(x,y,z)? For the algorithmic specifics of how the error estimate is calculated, refer to Berk's paper. The error estimate is smaller in the case of starting after 100 ns because in the case where you consider all the data, you are calculating Rg of diffuse molecules and a micelle. You're considering two different states and thus your data are poorly converged with respect to that measurement. -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] radius of gyration
On 5/8/12 4:50 PM, dina dusti wrote: Dear Justin, Thank you very much from your help, but may I ask you to say me why the error estimate of Rg is very smaller than Rgx, Rgy, Rgz, Please? I didn't understand any thing from paper about this problem! The value of Rg is calculated from the (x,y,z) components of the molecule's size, which, since the molecule is tumbling through solution, vary quite a bit. Diffusion in three dimensions doesn't necessarily impact the size of the molecule directly and hence the value of Rg is not affected as strongly. For a more exact description of how things are calculated, you'd have to go through the code for a real mathematical proof. -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] Formyl parameters
Where does swissparam get its parameters for charmm? and does it use custom atomtypes for generic molecules? I have been using CGenFF-derived parameters for molecules that aren't in base c36 and I think it's working well for me... -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, My .pdb input file has a formyl group which is not defined in CHARMM27 and CHARMM36. So I got its .itp file through swissparam. Now I want to use its parametrs. As I read in gromacs.org , I need to include this .itp in .top file. How does it come when I have not got any .top file yet? Anybody can suggest me how I can use .itp file and solve my problem? Thanks in advance, 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
[gmx-users] system cooling down when runing NVE
Dear Gromacs experts, I'm just a newbaby in Gromacs, and hence I have a lot of problem when running this program. I try to run NVE simulation of a protein. First, I run an NTP ensemble, follow by NVT and finally, NVE. In NPT and NVT, T remains as constant, however, in NVE simulation, the temperature drops gradually instead of maintain approximately constant. Could you give me any advice to solve this problem? Thank you very much. Regards, Nguyen P.S: below is my mdp file for three simulations: NPT ensemble: title = DEN2pro_MD define = -DFLEXIBLE constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2000 ps. nstcomm = 1 nstxout = 5000 ; output coordinates every 10 ps nstvout = 5000 ; output velocities every 10 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 NVT ensemble title = DEN2pro_MD NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 10 ; 2 * 10 = 200 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed NVE ensemble: title = DEN2pro_MD NVE equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md-vv ; leap-frog integrator nsteps = 100 ; 2 * 100 = 2000 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.6 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rlistlong = 1.6 ;treatment of van der waals interactions vdwtype = Shift rvdw= 0.95 ; short-range van der Waals cutoff (in nm) rvdw-switch = 0.9 ; Electrostatics coulombtype = PME-Switch; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = no
Re: [gmx-users] system cooling down when runing NVE
you have position restraints on, which I expect would damp collisions between solvent and solute. temp drops towards some sort of equilibrium, which doesn't necessarily match your starting temp even though energy of the system is conserved ..sounds like expected behavior to me? -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Thanh Binh NGUYEN nguye...@bii.a-star.edu.sg wrote: Dear Gromacs experts, I'm just a newbaby in Gromacs, and hence I have a lot of problem when running this program. I try to run NVE simulation of a protein. First, I run an NTP ensemble, follow by NVT and finally, NVE. In NPT and NVT, T remains as constant, however, in NVE simulation, the temperature drops gradually instead of maintain approximately constant. Could you give me any advice to solve this problem? Thank you very much. Regards, Nguyen P.S: below is my mdp file for three simulations: NPT ensemble: title = DEN2pro_MD define = -DFLEXIBLE constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2000 ps. nstcomm = 1 nstxout = 5000 ; output coordinates every 10 ps nstvout = 5000 ; output velocities every 10 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 NVT ensemble title = DEN2pro_MD NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps = 10 ; 2 * 10 = 200 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed NVE ensemble: title = DEN2pro_MD NVE equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md-vv ; leap-frog integrator nsteps = 100 ; 2 * 100 = 2000 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.6 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rlistlong = 1.6 ;treatment of van der waals interactions vdwtype = Shift rvdw = 0.95 ; short-range van der Waals cutoff (in nm) rvdw-switch = 0.9 ; Electrostatics coulombtype = PME-Switch; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = no; no temperature coupling in NVE ; Pressure coupling is off pcoupl = no
[gmx-users] radius of gyration
Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 9, 2012 4:52 AM Subject: Re: [gmx-users] radius of gyration On 5/8/12 4:50 PM, dina dusti wrote: Dear Justin, Thank you very much from your help, but may I ask you to say me why the error estimate of Rg is very smaller than Rgx, Rgy, Rgz, Please? I didn't understand any thing from paper about this problem! The value of Rg is calculated from the (x,y,z) components of the molecule's size, which, since the molecule is tumbling through solution, vary quite a bit. Diffusion in three dimensions doesn't necessarily impact the size of the molecule directly and hence the value of Rg is not affected as strongly. For a more exact description of how things are calculated, you'd have to go through the code for a real mathematical proof. -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] Formyl parameters
What do you mean? Am I supposed to use CGenFF to derive parameters? Cheers, Shima From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 9, 2012 5:20 AM Subject: Re: [gmx-users] Formyl parameters Where does swissparam get its parameters for charmm? and does it use custom atomtypes for generic molecules? I have been using CGenFF-derived parameters for molecules that aren't in base c36 and I think it's working well for me... -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear gmx users, My .pdb input file has a formyl group which is not defined in CHARMM27 and CHARMM36. So I got its .itp file through swissparam. Now I want to use its parametrs. As I read in gromacs.org , I need to include this .itp in .top file. How does it come when I have not got any .top file yet? Anybody can suggest me how I can use .itp file and solve my problem? Thanks in advance, Shima -- 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
[gmx-users] Re: Fwd: HEME-cysteine gromacs simulation
Zhang Bing, I guess it is problem in your visualizers. Try to label the atom using VMD which goes well with most of the file types derived in GROMACS. I hope you'll see the atom as FE not just F. Thanks Peterson -- View this message in context: http://gromacs.5086.n6.nabble.com/Fwd-HEME-cysteine-gromacs-simulation-tp4957846p4962257.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
