Re: [gmx-users] Topology files for OPLSAA and RESP charges
Hello, I just read your message... As far as I know, the RESP charge method is mainly employed forthe AMBER force field and associated (GLYCAM, GAFF, etc). I would check first that RESP is compatible with the method employed to develop OPLS-AA. Note that the AmberTools provide some scripts to calculate RESP charges. I have also used the RED server (http://q4md-forcefieldtools.org/REDS/), which is quite convenient when you want to take into account different conformations of a same molecule. In all cases, you will need to provide to those tools the molecular electrostatic potential of your molecule. None of this tools can generate a Gromacs topology file, however. Regards, Nicolas Tanos C. C. Franca a écrit : Dear GROMACS users, I'm trying to start running jobs using RESP charges and OPLSAA force field but I am facing problems to generate the RESP charges and the topology files for the OPLSAA force field. Does someone knows a software to calculate the RESP charges for the ligands and/or, also, to generate the .itp files for OPLSAA ? With the best regards, Tanos C. C. Franca. attachment: nicolas_sapay.vcf-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] maximum cut-off in Minimum image convention
Dear users, I wish to ask a question regarding the maximum cut-off in the minimum image convention (MIC). According to my understanding, MIC ensures that the separation between two particles i and j along each coordinate axes, namely, xi- xj, yi-yj, and zi-zj, is in the interval (-0.5L, 0.5L), where L is the box length (assumed the box to be cubic). This implies that distance rij can vary between 0 and 0.5L*sqrt(3). In order words the maximum separation should be less than half the diagonal: for example if i is located at (0,0,0) and j is located at the corner (0.49L, 0.49L, 0.49L). However, I read a couple of text books and online notes that claim that if r 0.5L, then MIC is violated. Specifically, this means that 0.5L rij 0.5L*sqrt(3) violates MIC. I find this confusing. I have been grinding hard to understand this point but I just cannot figure it out. In short my claim is that in MIC, rij can be at most half the diagonal length whereas the textbook says that rij can be at most half the box length. If I am wrong, can someone explain the flaw in my argument? Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] coarse grain dynamics
thanks all for the discussion. On Tue, May 25, 2010 at 5:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Thanks for the comments and info, but is there any way to take a particular frame for eg. the last frame of CG simulation and extend the run into all-atom simulation further ... There are tools out there to reconstruct an atomistic representation of a CG system (see link below, and poke around Google for a few minutes). If you want to start a whole new simulation, that is certainly possible after (of course) regenerating your system topology to match the new system. -Justin On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson thomp...@purdue.edu wrote: I agree with Justin on this one. Simulations run using CG that is not optimized for reconstruction may not actually reflect the type of interactions you are looking for. The current result of this simulation may not directly correspond to a full atomistic result, so even if a reconstruction were performed you would most likely NOT be able to draw conclusions from it. Otherwise, everyone would run really fast simulations in CG, then reconstruct their systems afterward. :) Quoting Justin A. Lemkul jalem...@vt.edu: ram bio wrote: thanks, but i am using gromacs version 4.0.07 I think the general consensus thus far is you won't be able to do what you want without significant effort to reconstruct your system, and perhaps then you should question whether any tools that seek to build optimal hydrogens from CG structures are going to bias the result. Would those hydrogen bonds have actually formed in an AA simulation? Hard to tell. If you want to analyze hydrogen bonds, CG approximations are not probably sufficient. This is a good exercise in planning your analysis before conducting your simulation. You can probably estimate some sort of polar contacts from your CG representation, but not hydrogen bonds. -Justin On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi egv...@gmail.com wrote: Hi, To change between representations (atomistic -- coarse grained), if you are using the MARTINI FF, you can use the modified version of Gromacs 3.3, check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt If you don't want to switch to full-atomistic representation, check which CG atom types are able to form hydrogen bonds and look for interactions between them. Obviously, this will be an approximation. Esteban G. Vega-Hissi UNSL San Luis Argentina -- On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson thomp...@purdue.edu wrote: There are programs around for reconstruction of full-atomistic representations from coarse-grained representations, however. I don't know if there are any available for the GROMACS architecture. Quoting Nuno Azoia naz...@det.uminho.pt: Hi there! I never worked with coarse grain simulations, but if you used a coarse grain methodology you didn't include all the atoms, so you didn't included hydrogens. So now you can not see them, of course. They are not there. If you need to know the hydrogen bond interactions you need to do some all atoms simulation, not coarse grain. Nuno Azoia On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote: Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like to know the hydrogen bond interactions between these two peptides. Please let me know how to do this, i can visualize the trajectory in VMD, but unable to calculate the hydrogen bonding distance and the hydrogen bonds existing.. Thanks Ram -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em Acabamento Departamento de Engenharia Têxtil Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt http://nazoia.net -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users
[gmx-users] Query regarding g_rmsf and g_hbond
Dear friends, I have some query regarding g_rmsf and g_hbond 1) Through g_rmsf we can plot rmsf Vs atom number (it is by default) but i want to plot rmsf Vs time, how i can do that? 2) Through g_hbond we can plot number of H-bonds Vs Time (By default) but i want to plot number of h-bonds Vs residues. Is it possible? I tried all the flag given in manual :( but i din not got desire plots. Regards Rituraj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] stepsize too small: help to solve problem in GROMACS installation
Dear gmx-users, after my last message yesterday on the gmx-user list, I contacted the administrators of the machine on which Gromacs 4.0.7 has been installed. We performed several checks and concluded that probably the command mdrun_d on that machine has been badly compiled (Gromacs has been installed in double precision), whereas the command mdrun_mpi has been compiled correctly and works correctly. They have some problems in finding the error in that installation because they don't know GROMACS in details, so they would like to check the installation they made with people more expert on GROMACS installation. I'm pasting below the steps they made to install Gromacs 4.0.7 on this machine: : GSL INSTALLATION: ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19 --enable-static --enable-shared make make install FFTW INSTALLATION: ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322 --enable-mpi --enable-static --enable-shared --enable-threads --enable-sse2 make make install GROMACS INSTALLATION: export LDFLAGS=-L/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322/lib -L/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19/lib export CPPFLAGS=-I/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322/incl ude -I/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19/include export NCPU=8 ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gromacs-407 --with-gsl --enable-shared --enable-double make -j $NCPU make install make distclean ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gromacs-407 --program-suffix=_mpi --with-gsl --enable-mpi --enable-double make mdrun -j $NCPU make install-mdrun Could anybody of you help us for the debugging of this installation? Many thanks again and best regards Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Query regarding g_rmsf and g_hbond
rituraj purohit skrev: Dear friends, I have some query regarding g_rmsf and g_hbond 1) Through g_rmsf we can plot rmsf Vs atom number (it is by default) but i want to plot rmsf Vs time, how i can do that? 2) Through g_hbond we can plot number of H-bonds Vs Time (By default) but i want to plot number of h-bonds Vs residues. Is it possible? I tried all the flag given in manual :( but i din not got desire plots. Regards Rituraj I think I implemented this feature in g_hbond at some point, but I never pushed it to the master branch. I'll see what I can dig up from the vaults. Until then you can in principle extract that information from the -hbn and -hbm output. As for the rmsf issue, isn't this what you get from g_rms? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] stepsize too small: help to solve problem in GROMACS installation
Anna Marabotti wrote: Dear gmx-users, after my last message yesterday on the gmx-user list, I contacted the administrators of the machine on which Gromacs 4.0.7 has been installed. We performed several checks and concluded that probably the command mdrun_d on that machine has been badly compiled (Gromacs has been installed in double precision), whereas the command mdrun_mpi has been compiled correctly and works correctly. They have some problems in finding the error in that installation because they don't know GROMACS in details, so they would like to check the installation they made with people more expert on GROMACS installation. I'm pasting below the steps they made to install Gromacs 4.0.7 on this machine: : GSL INSTALLATION: ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19 --enable-static --enable-shared make make install FFTW INSTALLATION: ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322 --enable-mpi --enable-static --enable-shared --enable-threads --enable-sse2 make make install GROMACS INSTALLATION: export LDFLAGS=-L/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322/lib -L/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19/lib export CPPFLAGS=-I/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322/include -I/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19/include export NCPU=8 ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gromacs-407 --with-gsl --enable-shared --enable-double make -j $NCPU make install make distclean ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gromacs-407 --program-suffix=_mpi --with-gsl --enable-mpi --enable-double make mdrun -j $NCPU make install-mdrun Could anybody of you help us for the debugging of this installation? Assuming that gcc-412 implies that the compiler is gcc-4.1.2, then you should take note of the big, bold warning on the Gromacs Downloads page: WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. -Justin Many thanks again and best regards Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it mailto:anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: the output of do_dssp
Hsin-Lin wrote: Hi, Justin Thank you for your patience. According your reply, I used trjconv to write only protein group into another file. I execute do_dssp again in group “protein”and “mainchain” respectively but still get coils more than total residues. Can you post the text of your coordinate file (preferably not as an attachment, just copy and paste it into an email)? -Justin Why? Hsin-Lin Hsin-Lin wrote: / Hi, Justin:/ / / / Thank you for your reply./ / I try to select the group, 'mainchain', when prompted, and get the quantity/ / of coil still larger than the number of residues of my protein./ Then some other elements of your system are being detected as containing relevant atoms. What happens if you run do_dssp on a single structure containing only your protein? / The data is the same as the output that generated by the selection, 1./ / Protein./ / If I select backbone, I get the fatal error: / / Failed to execute command: /Prousr/statphys/hsinlin/dssp/dsspcmbi -na/ / ddhIPvCe ddJ6Yv7a /dev/null 2 /dev/null / / / / And I don't understand even if I can run the selection, backbone,/ / successfully./ No, you can't. / According the dssp web of wiki:/ / http://en.wikipedia.org/wiki/DSSP_%28protein%29/ / the hydrogen bonds are dicided by O, C, H, and N four atoms./ / How can we get dssp analysis by backbone that includes only NCCNCCNCC.?/ / / You can't - DSSP requires the presence of the carbonyl O in order to determine hydrogen bonding geometry. If you don't have a full carbonyl, the analysis fails. -Justin / Sincerely yours,/ / Hsin-Lin/ / Hsin-Lin wrote:/ / Hi,/ / / / I use do_dssp to generate xvg file collect the last line to make a plot./ / There are something written in this way:/ / --/ / @ s0 legend Structure/ / @ s1 legend Coil/ / @ s2 legend Bend/ / 0514 1/ / ---/ / My system is dimer and each peptide has 6 residue./ / Then you have a problem. Your output indicates 14 residues are in a/ / random/ / coil, so either you have more than 12 total residues, or something went/ / wrong/ / in/ / the dssp calculation./ / / / And the number I choose to analyze is 1. Protein./ / / / Perhaps this is why you had a problem. Normally, choosing Protein would/ / cause/ / the calculation to hang, but maybe that is not the case any more. See/ / here/ / for/ / the proper group to choose and the rationale:/ / / / http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp/ / / / Now I have a question, if I want to calculate the percentage of/ / secondary/ / structure./ / In the example above, is it calculated in this way 5/12=42%?/ / / / I'd question your results first...you don't have 12 residues in your/ / calculation, otherwise your protein is 14/12 = 117% random coil! Also/ / realize/ / that (by default) the Structure term only includes alpha helix, beta/ / strand,/ / bend, and turn. Other structural elements are not included. That may or/ / may/ / not be what you want, depending on the structural elements of your/ / protein./ / -Justin/ / / / Hsin-Lin/ / / / / -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] maximum cut-off in Minimum image convention
Francisco Garcia wrote: Dear users, I wish to ask a question regarding the maximum cut-off in the minimum image convention (MIC). According to my understanding, MIC ensures that the separation between two particles i and j along each coordinate axes, namely, xi- xj, yi-yj, and zi-zj, is in the interval (-0.5L, 0.5L), where L is the box length (assumed the box to be cubic). This implies that distance rij can vary between 0 and 0.5L*sqrt(3). In order words the maximum separation should be less than half the diagonal: for example if i is located at (0,0,0) and j is located at the corner (0.49L, 0.49L, 0.49L). However, I read a couple of text books and online notes that claim that if r 0.5L, then MIC is violated. Specifically, this means that 0.5L rij 0.5L*sqrt(3) violates MIC. I find this confusing. I have been grinding hard to understand this point but I just cannot figure it out. In short my claim is that in MIC, rij can be at most half the diagonal length whereas the textbook says that rij can be at most half the box length. If I am wrong, can someone explain the flaw in my argument? The box diagonal is the longest dimension across the unit cell, so indeed it would seem that you can have r 0.5L. Simplify your problem to 2 dimensions and the answer becomes very clear. If you have a particle in the center of this 2-D lattice, and you have a cutoff 0.5L, then you are counting interactions with other particles within the central unit cell and duplicating at least some of these interactions in the periodic image. See, for instance: http://cmt.dur.ac.uk/sjc/thesis_dlc/node60.html Extend the radius in that image ever so slightly, and particle 1 is going to interact with *both* particles 4 and 7, the latter being the periodic image of the same particle. Several textbooks also discuss this phenomenon in depth. -Justin Thanks! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: the output of do_dssp
Hi, Justin: I post my coordinate with protein translated by trjconv By this gro file, I get 0 structure and 13 coils. regards, Hsin-Lin Generated by trjconv : Protein in water t= 0.0 144 1LEU N1 2.499 1.707 2.735 -0.1664 0.1749 0.5034 1LEU H12 2.496 1.753 2.824 -0.0517 -2.4571 1.9862 1LEU H23 2.456 1.619 2.755 0.1871 0.0557 0.7811 1LEU H34 2.591 1.691 2.698 -0.0836 0.9027 0.3938 1LEU CA5 2.419 1.772 2.633 -0.3054 -0.5208 0.2431 1LEU CB6 2.277 1.809 2.687 0.1445 -0.1872 -0.2452 1LEU CG7 2.202 1.686 2.731 -0.2024 0.3028 0.1044 1LEUCD18 2.063 1.737 2.778 0.2195 0.2407 0.1571 1LEUCD29 2.197 1.583 2.615 0.2120 -0.5339 0.1770 1LEU C 10 2.479 1.897 2.572 0.1063 -0.1920 0.0451 1LEU O 11 2.483 2.008 2.627 0.2017 -0.4490 0.0233 2TYR N 12 2.493 1.882 2.437 -0.1877 -0.3169 -0.5678 2TYR H 13 2.446 1.812 2.384 0.6045 -1.4218 0.1228 2TYR CA 14 2.568 1.987 2.363 -0.2499 0.5688 -0.4543 2TYR CB 15 2.589 1.933 2.224 0.6646 -0.2988 -0.3037 2TYR CG 16 2.641 2.031 2.122 0.0017 0.2452 -0.1870 2TYRCD1 17 2.772 2.065 2.121 -0.4594 -0.2211 -0.0739 2TYRHD1 18 2.841 2.029 2.196 -0.1936 2.1660 0.9115 2TYRCD2 19 2.561 2.096 2.031 0.6321 -0.0604 0.5143 2TYRHD2 20 2.454 2.077 2.025 0.6551 0.1338 -0.9454 2TYRCE1 21 2.827 2.158 2.032 -0.1241 0.2352 -0.6043 2TYRHE1 22 2.935 2.169 2.027 -0.0121 -0.2184 0.4867 2TYRCE2 23 2.607 2.183 1.935 -0.7318 -0.3641 0.2984 2TYRHE2 24 2.537 2.240 1.874 2.4629 1.6445 -1.8271 2TYR CZ 25 2.744 2.223 1.938 -0.9702 -0.5296 0.3816 2TYR OH 26 2.796 2.320 1.854 0.1652 0.2056 -0.1630 2TYR HH 27 2.714 2.370 1.829 -0.0067 -0.1509 -0.3161 2TYR C 28 2.492 2.121 2.359 -0.9847 -0.4718 -0.5034 2TYR O 29 2.369 2.129 2.344 0.1513 0.3775 -0.1130 3GLN N 30 2.564 2.228 2.385 -0.2495 0.1552 0.8649 3GLN H 31 2.647 2.221 2.441 -0.1774 -3.6419 0.5524 3GLN CA 32 2.519 2.362 2.357 0.6342 0.0752 -0.4227 3GLN CB 33 2.615 2.451 2.432 0.3037 -0.2198 0.6973 3GLN CG 34 2.569 2.596 2.453 -0.2200 0.0688 -0.5109 3GLN CD 35 2.556 2.690 2.327 0.9953 0.3411 -0.2090 3GLNOE1 36 2.640 2.694 2.240 -0.9468 -0.2495 -0.6126 3GLNNE2 37 2.449 2.761 2.321 -0.4839 0.0971 -0.2517 3GLN HE21 38 2.384 2.757 2.397 -0.8822 0.9806 -0.5342 3GLN HE22 39 2.443 2.818 2.239 1.3155 1.4839 0.4945 3GLN C 40 2.501 2.401 2.207 0.2212 -0.2300 0.2782 3GLN O 41 2.596 2.416 2.125 -0.3813 -0.0351 0.0925 4LEU N 42 2.377 2.427 2.177 -0.1825 0.0192 -0.2668 4LEU H 43 2.302 2.432 2.243 1.4715 -0.4825 1.7638 4LEU CA 44 2.342 2.451 2.033 0.2037 0.0368 -0.1113 4LEU CB 45 2.230 2.360 1.985 -0.4049 -0.4174 -0.1918 4LEU CG 46 2.193 2.374 1.838 0.7678 -0.3161 0.4261 4LEUCD1 47 2.243 2.255 1.755 0.7379 0.9397 0.6576 4LEUCD2 48 2.041 2.401 1.828 -0.2357 0.6221 -0.0518 4LEU C 49 2.300 2.600 2.014 0.1156 -0.7579 0.2678 4LEU O 50 2.183 2.641 2.032 0.0777 -0.1884 0.5428 5GLU N 51 2.402 2.676 1.977 0.1065 0.0801 -0.1886 5GLU H 52 2.499 2.669 2.001 -0.3871 0.9888 2.3980 5GLU CA 53 2.367 2.813 1.924 -0.4424 0.3677 0.0128 5GLU CB 54 2.465 2.914 1.989 -0.0708 -0.1784 0.3292 5GLU CG 55 2.431 3.059 2.017 0.0676 0.0058 -0.4907 5GLU CD 56 2.423 3.160 1.897 -0.1295 0.3354 0.1946 5GLUOE1 57 2.530 3.183 1.835 0.3233 -0.4874 0.7816 5GLUOE2 58 2.313 3.196 1.854 0.6508 -0.0618 0.6984 5GLU C 59 2.391 2.807 1.773 0.6638 -0.1591 -0.6210 5GLU O 60 2.500 2.836 1.726 -0.0179 -0.4997 -0.0116 6ASN N 61 2.278 2.810 1.704 -0.1838 -0.0571 0.1524 6ASN H 62 2.193 2.843 1.747 -1.7146 -1.5150 -1.5696 6ASN CA 63 2.278 2.779 1.562 -0.0805 -0.8216 0.6185 6ASN CB 64 2.200 2.652 1.531 -0.5886 -0.3894 -0.0808 6ASN CG 65 2.285 2.528 1.538 -0.1917 0.0598 0.1828 6ASNOD1 66 2.367 2.510 1.624 -0.1949 0.0958 0.2131 6ASNND2 67 2.262 2.432 1.453 -0.0713 0.3669 0.1154 6ASN HD21 68 2.176 2.451 1.407 -1.5107 -0.4210 2.3205 6ASN HD22 69 2.323 2.356 1.434 -0.8178 -0.7718 1.9579 6ASN C 70 2.223 2.893
Re: [gmx-users] Re: the output of do_dssp
Hsin-Lin Chiang wrote: Hi, Justin: I post my coordinate with protein translated by trjconv By this gro file, I get 0 structure and 13 coils. Analyze both chains separately using index groups. I would also encourage you to file a bugzilla about this issue. If you consider residues 1-6 and 7-12 separately, you get sensible output (6 residues in each). For some reason, if the two chains are combined and considered as a continuous structure, you get an extra residue, probably related to the termini. -Justin regards, Hsin-Lin Generated by trjconv : Protein in water t= 0.0 144 1LEU N1 2.499 1.707 2.735 -0.1664 0.1749 0.5034 1LEU H12 2.496 1.753 2.824 -0.0517 -2.4571 1.9862 1LEU H23 2.456 1.619 2.755 0.1871 0.0557 0.7811 1LEU H34 2.591 1.691 2.698 -0.0836 0.9027 0.3938 1LEU CA5 2.419 1.772 2.633 -0.3054 -0.5208 0.2431 1LEU CB6 2.277 1.809 2.687 0.1445 -0.1872 -0.2452 1LEU CG7 2.202 1.686 2.731 -0.2024 0.3028 0.1044 1LEUCD18 2.063 1.737 2.778 0.2195 0.2407 0.1571 1LEUCD29 2.197 1.583 2.615 0.2120 -0.5339 0.1770 1LEU C 10 2.479 1.897 2.572 0.1063 -0.1920 0.0451 1LEU O 11 2.483 2.008 2.627 0.2017 -0.4490 0.0233 2TYR N 12 2.493 1.882 2.437 -0.1877 -0.3169 -0.5678 2TYR H 13 2.446 1.812 2.384 0.6045 -1.4218 0.1228 2TYR CA 14 2.568 1.987 2.363 -0.2499 0.5688 -0.4543 2TYR CB 15 2.589 1.933 2.224 0.6646 -0.2988 -0.3037 2TYR CG 16 2.641 2.031 2.122 0.0017 0.2452 -0.1870 2TYRCD1 17 2.772 2.065 2.121 -0.4594 -0.2211 -0.0739 2TYRHD1 18 2.841 2.029 2.196 -0.1936 2.1660 0.9115 2TYRCD2 19 2.561 2.096 2.031 0.6321 -0.0604 0.5143 2TYRHD2 20 2.454 2.077 2.025 0.6551 0.1338 -0.9454 2TYRCE1 21 2.827 2.158 2.032 -0.1241 0.2352 -0.6043 2TYRHE1 22 2.935 2.169 2.027 -0.0121 -0.2184 0.4867 2TYRCE2 23 2.607 2.183 1.935 -0.7318 -0.3641 0.2984 2TYRHE2 24 2.537 2.240 1.874 2.4629 1.6445 -1.8271 2TYR CZ 25 2.744 2.223 1.938 -0.9702 -0.5296 0.3816 2TYR OH 26 2.796 2.320 1.854 0.1652 0.2056 -0.1630 2TYR HH 27 2.714 2.370 1.829 -0.0067 -0.1509 -0.3161 2TYR C 28 2.492 2.121 2.359 -0.9847 -0.4718 -0.5034 2TYR O 29 2.369 2.129 2.344 0.1513 0.3775 -0.1130 3GLN N 30 2.564 2.228 2.385 -0.2495 0.1552 0.8649 3GLN H 31 2.647 2.221 2.441 -0.1774 -3.6419 0.5524 3GLN CA 32 2.519 2.362 2.357 0.6342 0.0752 -0.4227 3GLN CB 33 2.615 2.451 2.432 0.3037 -0.2198 0.6973 3GLN CG 34 2.569 2.596 2.453 -0.2200 0.0688 -0.5109 3GLN CD 35 2.556 2.690 2.327 0.9953 0.3411 -0.2090 3GLNOE1 36 2.640 2.694 2.240 -0.9468 -0.2495 -0.6126 3GLNNE2 37 2.449 2.761 2.321 -0.4839 0.0971 -0.2517 3GLN HE21 38 2.384 2.757 2.397 -0.8822 0.9806 -0.5342 3GLN HE22 39 2.443 2.818 2.239 1.3155 1.4839 0.4945 3GLN C 40 2.501 2.401 2.207 0.2212 -0.2300 0.2782 3GLN O 41 2.596 2.416 2.125 -0.3813 -0.0351 0.0925 4LEU N 42 2.377 2.427 2.177 -0.1825 0.0192 -0.2668 4LEU H 43 2.302 2.432 2.243 1.4715 -0.4825 1.7638 4LEU CA 44 2.342 2.451 2.033 0.2037 0.0368 -0.1113 4LEU CB 45 2.230 2.360 1.985 -0.4049 -0.4174 -0.1918 4LEU CG 46 2.193 2.374 1.838 0.7678 -0.3161 0.4261 4LEUCD1 47 2.243 2.255 1.755 0.7379 0.9397 0.6576 4LEUCD2 48 2.041 2.401 1.828 -0.2357 0.6221 -0.0518 4LEU C 49 2.300 2.600 2.014 0.1156 -0.7579 0.2678 4LEU O 50 2.183 2.641 2.032 0.0777 -0.1884 0.5428 5GLU N 51 2.402 2.676 1.977 0.1065 0.0801 -0.1886 5GLU H 52 2.499 2.669 2.001 -0.3871 0.9888 2.3980 5GLU CA 53 2.367 2.813 1.924 -0.4424 0.3677 0.0128 5GLU CB 54 2.465 2.914 1.989 -0.0708 -0.1784 0.3292 5GLU CG 55 2.431 3.059 2.017 0.0676 0.0058 -0.4907 5GLU CD 56 2.423 3.160 1.897 -0.1295 0.3354 0.1946 5GLUOE1 57 2.530 3.183 1.835 0.3233 -0.4874 0.7816 5GLUOE2 58 2.313 3.196 1.854 0.6508 -0.0618 0.6984 5GLU C 59 2.391 2.807 1.773 0.6638 -0.1591 -0.6210 5GLU O 60 2.500 2.836 1.726 -0.0179 -0.4997 -0.0116 6ASN N 61 2.278 2.810 1.704 -0.1838 -0.0571 0.1524 6ASN H 62 2.193 2.843 1.747 -1.7146 -1.5150 -1.5696 6ASN CA 63 2.278 2.779 1.562 -0.0805 -0.8216 0.6185 6ASN CB 64 2.200 2.652 1.531
[gmx-users] analysis of md run results
Hello Justin, The energy values I get differ mainly for LJ and coulomb(SR) terms. I read through chapter 4 of manual but I did not find the difference between LJ/coulomb 1-4 and SR. 1-Where can I read about the differences of these? 2-Do you think the difference in energies as a result of excluding intramolecualr nonbonded interactions are reasonable? 3-I can not figure out why pressure in the first case in negative and it is very large when exclusions are included.Also in the second case kinetic energy is zero. :( 4-If I want to perform NPT simulation, the only thing I need to do is to switch on Pcoupl option in mdp file? Thank you for your help. No exclusions: mdrun -s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr* -x trajectoy.xtc *-c Hexane-Stack125_after_md -v output.mdrun_md g_energy -f ener.edr -o energy.xvg: tatistics over 5001 steps [ 0. thru 10. ps ], 13 data sets The term 'Cons. rmsd ()' is averaged over 501 frames All other averages are exact over 5001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Angle 4400.14259.533194.60259.4737 594.856 Ryckaert-Bell. 1000.11115.31888.7683 25.494 254.991 LJ-14 648.737.687236.55953.16904 31.6967 Coulomb-14 -281.38732.3948 12.46810.3554 103.574 *LJ (SR)-3322.5446.101140.96097.32669 73.2816 Coulomb (SR)667.86726.5968 9.4795 -8.60663 -86.0835* Coul. recip.921.79126.64078.48573 -8.74618 -87.4793 *Potential 4034.68386.493290.055 88.466 884.837* Kinetic En. 6336.76250.507237.56727.5244 275.299 Total Energy10371.4 561.13 450.23 115.99 1160.14 Temperature 297.59211.764511.15681.29262 12.9288 P*ressure (bar) -37.04171165.581161.54 -33.5839 -335.906* Cons. rmsd ()3.74741e-06 2.92095e-07 2.34721e-07 6.02133e-08 6.02253e-07 Heat Capacity Cv: 12.5011 J/mol K (factor = 0.00156281) run with exclusions in top file: mdrun -*rerun trajectoy.xtc* -s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr -c Hexane-Stack125_after_md -v output.mdrun_md Statistics over 5001 steps [ 0. thru 10. ps ], 13 data sets All averages are over 501 frames Energy Average RMSD Fluct. Drift Tot-Drift --- Angle 4400.09284.259237.26854.2184 542.293 Ryckaert-Bell. 1009.62124.46894.037928.2417 282.474 LJ-14 648.41140.6844 39.9262.70793 27.0848 Coulomb-14 -278.65434.422711.807111.1987 112.01 *LJ (SR)-3010.16 47.96842.53887.67736 76.789 Coulomb (SR)74.7846 2.51862.47007 0.170417 1.70451* Coul. recip. -78.04362.586061.54725 -0.717662 -7.17805 Potential 2766.05454.268342.141103.497 1035.18 Kinetic En. 0 0 0 0 0 Total Energy2766.05454.268342.141103.497 1035.18 *Temperature 0 0 0 0 0 Pressure (bar) 1973.01177.068172.80313.3792 133.819* Cons. rmsd () 0 0 0 0 0 Heat Capacity Cv: nan J/mol K (factor = nan) with: mdp file Electrostatics/VdW coulombtype = PME vdw-type= cut-off ;Cut-offs rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ;Temperature couplingBerendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = HEX ;sol tau_t = 0.1 ;0.1 ref_t = 300 ;300 ;Pressure coupling: Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ;Velocity generationGenerate velocites is on at 300 K. Manual p155 gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs pbc=xyz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] analysis of md run results
Moeed wrote: Hello Justin, The energy values I get differ mainly for LJ and coulomb(SR) terms. I read through chapter 4 of manual but I did not find the difference between LJ/coulomb 1-4 and SR. 1-Where can I read about the differences of these? For starters: http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy Also realize that 1-4 interactions are intramolecular, SR are intermolecular. The manual does explain these interactions. For additional reading, any basic MD textbook will undoubtedly discuss potential energy, its components, and how they're calculated. The Gromacs manual should provide some references as well. 2-Do you think the difference in energies as a result of excluding intramolecualr nonbonded interactions are reasonable? I have no basis to assess that. 3-I can not figure out why pressure in the first case in negative and it is very large when exclusions are included.Also in the second case kinetic energy is zero. :( For an NVT ensemble, pressure is basically meaningless. Even in the presence of pressure coupling, it will fluctuate quite a bit. http://www.gromacs.org/Documentation/Terminology/Pressure Since pressure is related to the virial, and the virial is affected by exclusions, you will see a difference. http://www.gromacs.org/Documentation/Terminology/Virial The temperature will be zero in the rerun energy file because the .xtc file does not contain velocities. If you rerun from a .trr file that has velocities, you should get a temperature term. 4-If I want to perform NPT simulation, the only thing I need to do is to switch on Pcoupl option in mdp file? Yes. Thank you for your help. No exclusions: mdrun -s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr* _-x trajectoy.xtc_ *-c Hexane-Stack125_after_md -v output.mdrun_md g_energy -f ener.edr -o energy.xvg: tatistics over 5001 steps [ 0. thru 10. ps ], 13 data sets The term 'Cons. rmsd ()' is averaged over 501 frames All other averages are exact over 5001 steps 10 ps may or may not be sufficient to equilibrate your system. By the looks of it, you haven't even reached your desired temperature yet. Energy Average RMSD Fluct. Drift Tot-Drift --- Angle 4400.14259.533194.60259.4737 594.856 Ryckaert-Bell. 1000.11115.31888.7683 25.494 254.991 LJ-14 648.737.687236.55953.16904 31.6967 Coulomb-14 -281.38732.3948 12.46810.3554 103.574 *LJ (SR)-3322.5446.101140.96097.32669 73.2816 Coulomb (SR)667.86726.5968 9.4795 -8.60663 -86.0835* Coul. recip.921.79126.64078.48573 -8.74618 -87.4793 *Potential 4034.68386.493290.055 88.466 884.837* Kinetic En. 6336.76250.507237.56727.5244 275.299 Total Energy10371.4 561.13 450.23 115.99 1160.14 Temperature 297.59211.764511.15681.29262 12.9288 P*ressure (bar) -37.04171165.581161.54 -33.5839 -335.906* Cons. rmsd ()3.74741e-06 2.92095e-07 2.34721e-07 6.02133e-08 6.02253e-07 Heat Capacity Cv: 12.5011 J/mol K (factor = 0.00156281) run with exclusions in top file: mdrun -*rerun trajectoy.xtc* -s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr -c Hexane-Stack125_after_md -v output.mdrun_md Statistics over 5001 steps [ 0. thru 10. ps ], 13 data sets All averages are over 501 frames Energy Average RMSD Fluct. Drift Tot-Drift --- Angle 4400.09284.259237.26854.2184 542.293 Ryckaert-Bell. 1009.62124.46894.037928.2417 282.474 LJ-14 648.41140.6844 39.9262.70793 27.0848 Coulomb-14 -278.65434.422711.807111.1987 112.01 *LJ (SR)-3010.16 47.96842.5388 7.67736 76.789 Coulomb (SR)74.7846 2.51862.47007 0.170417 1.70451* Coul. recip. -78.04362.586061.54725 -0.717662 -7.17805 Potential 2766.05454.268342.141103.497 1035.18 Kinetic En. 0 0 0 0 0 Total Energy2766.05454.268342.141103.497 1035.18 *Temperature 0 0 0 0 0 Pressure (bar) 1973.01177.068172.80313.3792 133.819* Cons. rmsd () 0 0 0 0 0 Heat Capacity Cv: nan
[gmx-users] Re: PMF in vacuum (chris.ne...@utoronto.ca)
Hello Chris, thanks for your attention. I'm sending you some links to some tests I performed. As I said you will notice that depending on the parameter used my simulation shows PMF profiles quite different. Especially what concerns to the difference between the use or not of the PBC. https://sites.google.com/site/fileti/files/test1.jpg https://sites.google.com/site/fileti/files/test2.jpg https://sites.google.com/site/fileti/files/histo.png I have constructed two very similar topologies (ben-a.itp and ben-b.itp) where I put a virtual site in the center of benzene. This sites were restrained to keep my molecules fixed distance desired. The basic details of the simulations are given below:1000 define = -DPOSRES integrator = sd tinit= 0 dt = 0.002 nsteps = 500 or 50 comm-mode= angular nstcomm = 1 comm-grps= System bd-fric = 1 ld-seed = 1993 nstlist = 5 ns_type = simple pbc = no or xyz periodic_molecules = no rlist= 0 coulombtype = Cut-off vdw-type = Cut-off rvdw = 0 DispCorr = no Tcoupl = Nose-Hoover tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 constraints = all-bonds constraint_algorithm = lincs ; COM PULLING pull = umbrella pull_geometry= distance pull_dim = N N Y pull_r1 = 1 pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = BENa pull_weights0= pull_pbcatom0= 0 pull_group1 = BENb pull_weights1= pull_pbcatom1= 0 pull_vec1= 0 0 1 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1700 or ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br Dear Eudes: Can you please elaborate on your description? What .mdp options are you using? What exactly do your curves look like (you can post pictures to photobucket or some other online service and link them here)? If you suspect that you are doing something wrong, then we need to understand exactly what you are doing and exactly what you are seeing in order to help. Chris. -- original message -- Hi gmx-users, I'm trying to simulate a umbrella sampling PMF between two benzene molecules in vacuum. My protocol is working fine, my histograms have good overlap and the curves I have got are quite reasonable. However I have noticed that some options in my .mdp file can significantly change the depth of the well. Also the curves can not go to zero at long distances. For example, if I use PBC I get a reasonably good value for the minimum of the PMF but from a certain separation it starts to increase slightly in a linear fashion instead of going to zero. On the other hand, if I make pbc = no, I get an acceptable curve, with the PMF going to zero, but with the minimum too high. Someone could give me any tips on the best set of parameters to calculate this PMF in a vacuum? bests eef -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: the output of do_dssp
- Original Message - From: Hsin-Lin Chiang jian...@phys.sinica.edu.tw Date: Thursday, May 27, 2010 0:28 Subject: [gmx-users] Re: the output of do_dssp To: gmx-users@gromacs.org Hi, Justin: I post my coordinate with protein translated by trjconv By this gro file, I get 0 structure and 13 coils. Haven't you been saying for what seems like weeks now that you have 12 residues in your protein? If so... snip C 70 2.223 2.893 1.484 -0.0883 0.1244 -0.1837 6ASN O1 71 2.111 2.941 1.505 -0.2557 -0.4837 -0.1041 6ASN O2 72 2.313 2.953 1.419 - 0.5561 0.0660 0.4455 Here, there's quite clearly an internal COO and NH3... hence it seems that you have two 6-residue chains. That's important data to be aware of, and to communicate to people who might help... Our belief that you really had a 12-residue peptide excludes this kind of issue from trouble-shooting, which ends up wasting everyone's time. Mark 7LEU N 73 1.111 2.804 2.186 0.3062 -0.5955 -0.0550 7LEU H1 74 1.174 2.856 2.129 0.2303 -0.3221 0.1077 7LEU H2 75 1.019 2.834 2.164 0.0461 -1.9085 -0.8807 7LEU H3 76 1.126 2.815 2.284 0.4122 -2.4532 0.1866 snip -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Non-conservation of total energy while using structure file to resume the simulation
Dear GMX'ers! I simulate system of about hundreds of water molecules in NVE ensemble with md integrator. Every 100 ps I need to change slightly some parameters, say, electric field and to continue the simulation from this point. As I realize I cannot go on my run using the checkpointing and tpbconv in this case. Therefore I try to use the output structure file confout.gro which contains both coordinates and velocities at the end of the previous step. The problem is in the total energy. Within every 100-ps run the energy drift is quite low. But when I start the next step, at its very beginning I see the considerable jump in the total energy and the temperature comparing with the end values of previuos step. NOTE that it is the case even when I change NOTHING in my job.mdp file! To my knowledge the coordinates and velocities define exactly the energy and the temperature. Now I suspect the only reason - low precision of confout.gro. So, my questions are: Is there another reason for the total energy non-conservation in my simulation? How can I get the full precision in output structure file RIGTH after mdrun? Or it is mandatory to use trjconv with -ndec option? What is the default precision of .trr trajectory file in single and double precision modes? Hoping for your help, -- Regards, Dmitri mailto:ddu...@ngs.ru-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CG (MARTINI) parameters for RNA
Shalom all, I wish to try and simulate a protein with few RNA bases attached. As I favour speed over accuracy in this case I wish to use the MARTINI model. I could not find RNA/DNA parameters, but noticed that on the site there is a reference to Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP. DNA and lipid bilayers: self-assembly and insertion. J. Royal Soc. Int. 5, S241-S250, 2008. I wonder if someone had those parameters already implemented into the model? It will be nice to get it nicely packed. Or maybe even better, are there any beta parameters to RNA/DNA in a new MARTINI force field? All the best, Itamar -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu.au -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation
- Original Message - From: Dmitri Dubov ddu...@ngs.ru Date: Thursday, May 27, 2010 15:41 Subject: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation To: Discussion list for GROMACS users gmx-users@gromacs.org Dear GMX'ers! I simulate system of about hundreds of water molecules in NVE ensemble with md integrator. Every 100 ps I need to change slightly some parameters, say, electric field and to continue the simulation from this point. As I realize I cannot go on my run using the checkpointing and tpbconv in this case. Therefore I try to use the output structure file confout.gro which contains both coordinates and velocities at the end of the previous step. The problem is in the total energy. Within every 100-ps run the energy drift is quite low. But when I start the next step, at its very beginning I see the considerable jump in the total energy and the temperature comparing with the end values of previuos step. NOTE that it is the case even when I change NOTHING in my job.mdp file! Sure, discontinuity is guaranteed from the loss of precision. To my knowledge the coordinates and velocities define exactly the energy and the temperature. Now I suspect the only reason - low precision of confout.gro. So, my questions are: Is there another reason for the total energy non-conservation in my simulation? Probably not. How can I get the full precision in output structure file RIGTH after mdrun? Or it is mandatory to use trjconv with -ndec option? I expect that either grompp -f new -o newtpr mdrun -s newtpr -cpi old_state.cpt or grompp -f new -t old_state.cpt -o newtpr mdrun -s newtpr will do what you want. Please report back if one or both work :-) Or, maybe you can use old-style .trr and .edr output as input to grompp, so long as you planned that in advance. A checkpoint-file approach is superior, however. What is the default precision of .trr trajectory file in single and double precision modes? Machine precision. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
