Re: [gmx-users] regarding the cosine content analysis
You don't do it the right way. You must start the analysis from the beginning not from the end of your trajectory. I.e. 0-20ns 0-30ns 0-40ns ... 0-100ns Until the cosine content of the first 3 principal components that account for most of the variance in the atomic fluctuation have been dropped at least once below 0.5. This is the point where theoretically the system has equilibrated enough. Thomas On 22 February 2013 13:43, Ahmet yıldırım wrote: > Dear users, > > I performed MD simulation of 400 ns of a structure. I used the cosine > content to check whether the simulation is not converged. I used last 100 > and 50 ns of trajectory to the analysis, respectively. The results were > very similar to each other.The cosine contents of the first ten principal > components are as follows. The cosine contents of the principal components > are very small but one. Why is the second cosine content differs from the > others? What could be the reason for this? And do you think simulation has > reached convergence? > > The cosine contents of last 50 ns: > 1 0.00685769 > 2 0.137028 > 3 0.00139929 > 4 0.00903137 > 5 0.0180072 > 6 0.0128686 > 7 0.00154502 > 8 9.71793e-05 > 9 0.00485945 > 10 0.00202377 > > Thanks in advance > -- > Ahmet Yıldırım > -- > 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 > -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] regarding the cosine content analysis
Hi Thomas, As I've explained previously, the cosine content does not allow such inferences. Besides, taking the relaxation from the start into account in PCA is pretty nonsensical, unless you aim to characterize that relaxation in the first place. Looking at the cosine content to infer equilibration from that is blatantly fooling yourself. If you feel you must use cosine content to support any claim on equilibration, then it is a much better approach to start from the end of the simulation and check that the stretch of the trajectory you take does not yield high cosine contents, in which case you have some reason to argue that that part of the simulation is sampled in a local equilibrium. Cheers, Tsjerk On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis wrote: > You don't do it the right way. You must start the analysis from the > beginning not from the end of your trajectory. I.e. > > 0-20ns > 0-30ns > 0-40ns > ... > 0-100ns > > Until the cosine content of the first 3 principal components that account > for most of the variance in the atomic fluctuation have been dropped at > least once below 0.5. This is the point where theoretically the system has > equilibrated enough. > > Thomas > > > On 22 February 2013 13:43, Ahmet yıldırım wrote: > >> Dear users, >> >> I performed MD simulation of 400 ns of a structure. I used the cosine >> content to check whether the simulation is not converged. I used last 100 >> and 50 ns of trajectory to the analysis, respectively. The results were >> very similar to each other.The cosine contents of the first ten principal >> components are as follows. The cosine contents of the principal components >> are very small but one. Why is the second cosine content differs from the >> others? What could be the reason for this? And do you think simulation has >> reached convergence? >> >> The cosine contents of last 50 ns: >> 1 0.00685769 >> 2 0.137028 >> 3 0.00139929 >> 4 0.00903137 >> 5 0.0180072 >> 6 0.0128686 >> 7 0.00154502 >> 8 9.71793e-05 >> 9 0.00485945 >> 10 0.00202377 >> >> Thanks in advance >> -- >> Ahmet Yıldırım >> -- >> 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 >> > > > > -- > > == > > Thomas Evangelidis > > PhD student > University of Athens > Faculty of Pharmacy > Department of Pharmaceutical Chemistry > Panepistimioupoli-Zografou > 157 71 Athens > GREECE > > email: tev...@pharm.uoa.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
AW: AW: [gmx-users] g_current
Hi, Which version of gromacs are you using. I am applying this tool also to ILs and it works fine for me in the release-4-5 branch. It is especially strange that you have a rotational dipole moment of zero. However, currently I have no idea where the segfault arises. Especially because you get an output. So what version you are using? Cheers, Flo > -Ursprüngliche Nachricht- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > Gesendet: Montag, 25. Februar 2013 00:05 > An: Discussion list for GROMACS users > Betreff: Re: AW: [gmx-users] g_current > > Hello, > > My system is ionic liquids composed of 128 cation (EMIM) and 128 anion (ethyl > sulfate). I choose system (0) as index group. > > Nilesh > > > Hi, > > > > Can you be a little bit more specific about your system, and what you > > have chosen as index groups ? > > > > /Flo > > > > --- > > Florian Dommert > > Dipl. Phys. > > > > Institut für Computerphysik > > Universität Stuttgart > > Allmandring 3 > > D-70569 Stuttgart > > > > Tel.: 0711-68563613 > > Fax: 0711-68563658 > > > >> -Ursprüngliche Nachricht- > >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > >> Gesendet: Samstag, 23. Februar 2013 16:17 > >> An: gmx-users@gromacs.org > >> Betreff: [gmx-users] g_current > >> > >> Hello, > >> > >> I am calculating the correlation of the rotational and translational > > dipole > >> moment of the system using g_current. > >> > >> I used following command > >> > >> g_current -f md.trr -s md.tpr mc > >> > >> It crashed with segmental fault. > >> Last frame 15000 time 3.002 > >> Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11 > >> > >> > >> Average translational dipole moment M_J [enm] after 15001 frames > >> (|M|^2): > >> -0.00 -0.00 -0.00 (0.00) > >> > >> > >> Average molecular dipole moment M_D [enm] after 15001 frames (|M|^2): > >> -7.281919 17.954138 5.845435 (490.493744) > >> > >> > >> > >> Absolute values: > >> epsilon=2723.718750 > >> , , <(M_J*M_D)^2>: (490.493744, 0.00, -0.03) > >> > >> > >> > >> > >> Fluctuations: > >> epsilon=450.336090 > >> > >> > >> deltaM_D , deltaM_J, deltaM_JD: (80.947235, 0.00, 0.00) > >> > >> > >> > >> Static dielectric constant using integral and fluctuations: > >> 450.336090 > >> > >> < M_JM_D > via integral: -0.000 > >> > >> *** > >> > >> Average volume V=42.031509 nm^3 at T=300.00 K and corresponding > >> refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975 > >> > >> Start fit at 98.08 ps (100.00). > >> End fit at 398.31 ps (400.00). > >> > >> Einstein-Helfand fit to the MSD of the translational dipole moment > >> yields: > >> > >> sigma=0. > >> translational fraction of M^2: 0. Dielectric constant using EH: > >> 2723.7188 Segmentation fault > >> > >> > >> Can you whats the problem? > >> > >> Nilesh > >> > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the www > > interface or > >> send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface or > send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] request
Dear Gromacs Users. I apologize for asking a question that has come up several times by numerous users in the previous e-mails, but I have read the answers and suggestions to those posts and I am not still able to solve the problem based on them. It is completely possible that I am just not seeing the obvious, so I apologize, but I would welcome any advice. I want to work on "Human Glutathione Peroxidase" and downloaded its pdb file, but when I try pdb2gmx, I face Fatal Error: Program pdb2gmx, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/pgutil.c, line: 91 Fatal error: Atom CD is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 50. I tried different force fields, for example OPLS-AA/L all-atom force field, different versions of AMBERs, but I always get the same problem! When I tried GROMOS's versions, the problem goes on CZ atom instead of CD. Here is a chunk of my pdb file (I have also attached the full pdb file to this e-mail): SHEET 6 A 1 PHE A 183 PRO A190 0 SHEET 7 A 1 GLY A 192 HIS A200 0 MODEL ATOM 1 N GLY A 38 -4.242 -9.833 -26.316 1.00 0.00 N ATOM 2 CA GLY A 38 -3.416 -10.949 -25.765 1.00 0.00 C ATOM 3 C GLY A 38 -1.953 -10.570 -25.632 1.00 0.00 C ATOM 4 O GLY A 38 -1.069 -11.266 -26.159 1.00 0.00 O ATOM 5 N THR A 39 -1.673 -9.461 -24.940 1.00 0.00 N ATOM 6 CA THR A 39 -0.286 -9.039 -24.705 1.00 0.00 C ATOM 7 C THR A 39 -0.073 -8.722 -23.214 1.00 0.00 C ATOM 8 O THR A 39 -1.035 -8.559 -22.442 1.00 0.00 O ATOM 9 CB THR A 39 0.124 -7.784 -25.533 1.00 0.00 C ATOM 10 OG1 THR A 39 -0.415 -6.602 -24.926 1.00 0.00 O ATOM 11 CG2 THR A 39 -0.309 -7.882 -27.037 1.00 0.00 C ….. ATOM 91 OD1 ASP A 49 10.106 1.841 -5.471 1.00 0.00 O ATOM 92 OD2 ASP A 49 12.010 2.918 -5.273 1.00 0.00 O ATOM 93 N GLY A 50 8.192 0.495 -3.643 1.00 0.00 N ATOM 94 CA GLY A 50 6.805 0.919 -3.449 1.00 0.00 C ATOM 95 C GLY A 50 6.525 2.278 -4.054 1.00 0.00 C ATOM 96 O GLY A 50 5.449 2.818 -3.864 1.00 0.00 O ATOM 97 N GLU A 51 7.471 2.832 -4.802 1.00 0.00 N ATOM 98 CA GLU A 51 7.351 4.238 -5.211 1.00 0.00 C ATOM 99 C GLU A 51 6.737 4.438 -6.592 1.00 0.00 C ATOM 100 O GLU A 51 6.291 5.522 -6.897 1.00 0.00 O ATOM 101 CB GLU A 51 8.713 4.941 -5.174 1.00 0.00 C ATOM 102 CG GLU A 51 9.283 5.140 -3.759 1.00 0.00 C ATOM 103 CD GLU A 51 8.612 6.301 -3.006 1.00 0.00 C ATOM 104 N GLU A 52 6.729 3.418 -7.432 1.00 0.00 N …. ATOM 3035 OH TYR A 228 -9.320 -43.377 -52.577 1.00 0.00 O TER3036 TYR A 228 ENDMDL HETATM 3037 CL CL 11000 -16.070 -39.525 -6.168 1.00 0.00 CL HETATM 3038 NA NA 11001 -1.679 -34.065 -0.491 1.00 0.00 NA CONECT 996 1519 CONECT 1021 1519 CONECT 1519 996 1021 END I know that the residue number printed by pdb2gmx is actually starting from zero, so the problem is actually in GLU. In both rtp file and pdb I have CD atom. Some suggestions wanted to change the order of C and O in pdb file, but it didn't work. What should I do? Thanks a lot. Groupgro. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] regarding the cosine content analysis
On 25 February 2013 12:14, Tsjerk Wassenaar wrote: > Hi Thomas, > > As I've explained previously, the cosine content does not allow such > inferences. Besides, taking the relaxation from the start into account > in PCA is pretty nonsensical, unless you aim to characterize that > relaxation in the first place. Looking at the cosine content to infer > Yes, that's what I meant, to identity those ns where the protein does unidirectional motion before it starts exploring the energy landscape, and exclude them from the final analysis (whatever this is). At least this is what I've seen doing in publications and this is what I have understood from our previous conversations. I think your objection is about the way I use the term "equilibration" to refer to what you call "relaxation" (I presume it is not the same as energy minimization). Perhaps it would be helpful to have your definition of the terms "equilibration" and "relaxation. > equilibration from that is blatantly fooling yourself. > If you feel you must use cosine content to support any claim on > equilibration, then it is a much better approach to start from the end > of the simulation and check that the stretch of the trajectory you > take does not yield high cosine contents, in which case you have some > reason to argue that that part of the simulation is sampled in a local > equilibrium. > > Cheers, > > Tsjerk > > > On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis > wrote: > > You don't do it the right way. You must start the analysis from the > > beginning not from the end of your trajectory. I.e. > > > > 0-20ns > > 0-30ns > > 0-40ns > > ... > > 0-100ns > > > > Until the cosine content of the first 3 principal components that account > > for most of the variance in the atomic fluctuation have been dropped at > > least once below 0.5. This is the point where theoretically the system > has > > equilibrated enough. > > > > Thomas > > > > > > On 22 February 2013 13:43, Ahmet yıldırım wrote: > > > >> Dear users, > >> > >> I performed MD simulation of 400 ns of a structure. I used the cosine > >> content to check whether the simulation is not converged. I used last > 100 > >> and 50 ns of trajectory to the analysis, respectively. The results were > >> very similar to each other.The cosine contents of the first ten > principal > >> components are as follows. The cosine contents of the principal > components > >> are very small but one. Why is the second cosine content differs from > the > >> others? What could be the reason for this? And do you think simulation > has > >> reached convergence? > >> > >> The cosine contents of last 50 ns: > >> 1 0.00685769 > >> 2 0.137028 > >> 3 0.00139929 > >> 4 0.00903137 > >> 5 0.0180072 > >> 6 0.0128686 > >> 7 0.00154502 > >> 8 9.71793e-05 > >> 9 0.00485945 > >> 10 0.00202377 > >> > >> Thanks in advance > >> -- > >> Ahmet Yıldırım > >> -- > >> 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 > >> > > > > > > > > -- > > > > == > > > > Thomas Evangelidis > > > > PhD student > > University of Athens > > Faculty of Pharmacy > > Department of Pharmaceutical Chemistry > > Panepistimioupoli-Zografou > > 157 71 Athens > > GREECE > > > > email: tev...@pharm.uoa.gr > > > > teva...@gmail.com > > > > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157
Re: [gmx-users] regarding the cosine content analysis
Hi, I think my question was misunderstood. My question is: Why is second cosine content greater than the other values? Regards 2013/2/25 Thomas Evangelidis > On 25 February 2013 12:14, Tsjerk Wassenaar wrote: > > > Hi Thomas, > > > > As I've explained previously, the cosine content does not allow such > > inferences. Besides, taking the relaxation from the start into account > > in PCA is pretty nonsensical, unless you aim to characterize that > > relaxation in the first place. Looking at the cosine content to infer > > > > Yes, that's what I meant, to identity those ns where the protein does > unidirectional motion before it starts exploring the energy landscape, and > exclude them from the final analysis (whatever this is). At least this is > what I've seen doing in publications and this is what I have understood > from our previous conversations. I think your objection is about the way I > use the term "equilibration" to refer to what you call "relaxation" (I > presume it is not the same as energy minimization). Perhaps it would be > helpful to have your definition of the terms "equilibration" and > "relaxation. > > > > equilibration from that is blatantly fooling yourself. > > If you feel you must use cosine content to support any claim on > > equilibration, then it is a much better approach to start from the end > > of the simulation and check that the stretch of the trajectory you > > take does not yield high cosine contents, in which case you have some > > reason to argue that that part of the simulation is sampled in a local > > equilibrium. > > > > Cheers, > > > > Tsjerk > > > > > > On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis > > wrote: > > > You don't do it the right way. You must start the analysis from the > > > beginning not from the end of your trajectory. I.e. > > > > > > 0-20ns > > > 0-30ns > > > 0-40ns > > > ... > > > 0-100ns > > > > > > Until the cosine content of the first 3 principal components that > account > > > for most of the variance in the atomic fluctuation have been dropped at > > > least once below 0.5. This is the point where theoretically the system > > has > > > equilibrated enough. > > > > > > Thomas > > > > > > > > > On 22 February 2013 13:43, Ahmet yıldırım wrote: > > > > > >> Dear users, > > >> > > >> I performed MD simulation of 400 ns of a structure. I used the cosine > > >> content to check whether the simulation is not converged. I used last > > 100 > > >> and 50 ns of trajectory to the analysis, respectively. The results > were > > >> very similar to each other.The cosine contents of the first ten > > principal > > >> components are as follows. The cosine contents of the principal > > components > > >> are very small but one. Why is the second cosine content differs from > > the > > >> others? What could be the reason for this? And do you think simulation > > has > > >> reached convergence? > > >> > > >> The cosine contents of last 50 ns: > > >> 1 0.00685769 > > >> 2 0.137028 > > >> 3 0.00139929 > > >> 4 0.00903137 > > >> 5 0.0180072 > > >> 6 0.0128686 > > >> 7 0.00154502 > > >> 8 9.71793e-05 > > >> 9 0.00485945 > > >> 10 0.00202377 > > >> > > >> Thanks in advance > > >> -- > > >> Ahmet Yıldırım > > >> -- > > >> 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 > > >> > > > > > > > > > > > > -- > > > > > > == > > > > > > Thomas Evangelidis > > > > > > PhD student > > > University of Athens > > > Faculty of Pharmacy > > > Department of Pharmaceutical Chemistry > > > Panepistimioupoli-Zografou > > > 157 71 Athens > > > GREECE > > > > > > email: tev...@pharm.uoa.gr > > > > > > teva...@gmail.com > > > > > > > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > > > post-doctoral researcher > > Biocomputing Group > > Department of Biological Sciences > > 2500 University Drive NW > > Calgary, AB T2N 1N4 > > Canada > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Maili
Re: [gmx-users] regarding the cosine content analysis
Hi Thomas, Okay :) First of all, do be careful that the first stage of relaxation, giving that nice principal component profile, is not exclusive. If you take it off, by leaving out the first part of the trajectory, you may well find that there is another component which is still relaxing, which maybe could only start after the first bit finished (think of rotation and hinging; maybe have to hinge a bit before the (other) rotation can relax). So checking cosine content from the start up to the point that you have a low correlation and then claiming that the system is relaxed after that is dangerous. What that relaxation and equilibrium is? Let's started by introducing the initial state T, as in T(ensed). That state can be a crystal structure, in which the packing forces cause it to adopt a structure that has a low probability under the conditions you're doing your simulations at. It could also be the result from (homology) modeling, where you can imagine a set of forces having acted to yield that structure. Of course the same set of forces is still present, but aimed outward from the protein if you change the environment. The system is sort of wound up as a spring, and that potential energy needs to dissipate before you can argue that the system samples conformations that reflect the underlying, unperturbed energy landscape. That's what the relaxation is: losing that initial strain and get onto the energy landscape proper. Equilibrium is of course a different matter still, where the actual conformations and their relative probabilities come into play. Cheers, Tsjerk On Mon, Feb 25, 2013 at 12:41 PM, Thomas Evangelidis wrote: > On 25 February 2013 12:14, Tsjerk Wassenaar wrote: > >> Hi Thomas, >> >> As I've explained previously, the cosine content does not allow such >> inferences. Besides, taking the relaxation from the start into account >> in PCA is pretty nonsensical, unless you aim to characterize that >> relaxation in the first place. Looking at the cosine content to infer >> > > Yes, that's what I meant, to identity those ns where the protein does > unidirectional motion before it starts exploring the energy landscape, and > exclude them from the final analysis (whatever this is). At least this is > what I've seen doing in publications and this is what I have understood > from our previous conversations. I think your objection is about the way I > use the term "equilibration" to refer to what you call "relaxation" (I > presume it is not the same as energy minimization). Perhaps it would be > helpful to have your definition of the terms "equilibration" and > "relaxation. > > >> equilibration from that is blatantly fooling yourself. >> If you feel you must use cosine content to support any claim on >> equilibration, then it is a much better approach to start from the end >> of the simulation and check that the stretch of the trajectory you >> take does not yield high cosine contents, in which case you have some >> reason to argue that that part of the simulation is sampled in a local >> equilibrium. >> >> Cheers, >> >> Tsjerk >> >> >> On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis >> wrote: >> > You don't do it the right way. You must start the analysis from the >> > beginning not from the end of your trajectory. I.e. >> > >> > 0-20ns >> > 0-30ns >> > 0-40ns >> > ... >> > 0-100ns >> > >> > Until the cosine content of the first 3 principal components that account >> > for most of the variance in the atomic fluctuation have been dropped at >> > least once below 0.5. This is the point where theoretically the system >> has >> > equilibrated enough. >> > >> > Thomas >> > >> > >> > On 22 February 2013 13:43, Ahmet yıldırım wrote: >> > >> >> Dear users, >> >> >> >> I performed MD simulation of 400 ns of a structure. I used the cosine >> >> content to check whether the simulation is not converged. I used last >> 100 >> >> and 50 ns of trajectory to the analysis, respectively. The results were >> >> very similar to each other.The cosine contents of the first ten >> principal >> >> components are as follows. The cosine contents of the principal >> components >> >> are very small but one. Why is the second cosine content differs from >> the >> >> others? What could be the reason for this? And do you think simulation >> has >> >> reached convergence? >> >> >> >> The cosine contents of last 50 ns: >> >> 1 0.00685769 >> >> 2 0.137028 >> >> 3 0.00139929 >> >> 4 0.00903137 >> >> 5 0.0180072 >> >> 6 0.0128686 >> >> 7 0.00154502 >> >> 8 9.71793e-05 >> >> 9 0.00485945 >> >> 10 0.00202377 >> >> >> >> Thanks in advance >> >> -- >> >> Ahmet Yıldırım >> >> -- >> >> 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...@g
Re: [gmx-users] regarding the cosine content analysis
Because it fits a little bit better to a cosine with full period than the first one fits a cosine with half period and the third one fits a cosine with 1.5 period. Tsjerk On Mon, Feb 25, 2013 at 1:23 PM, Ahmet yıldırım wrote: > Hi, > > I think my question was misunderstood. > My question is: > Why is second cosine content greater than the other values? > > Regards > > 2013/2/25 Thomas Evangelidis > >> On 25 February 2013 12:14, Tsjerk Wassenaar wrote: >> >> > Hi Thomas, >> > >> > As I've explained previously, the cosine content does not allow such >> > inferences. Besides, taking the relaxation from the start into account >> > in PCA is pretty nonsensical, unless you aim to characterize that >> > relaxation in the first place. Looking at the cosine content to infer >> > >> >> Yes, that's what I meant, to identity those ns where the protein does >> unidirectional motion before it starts exploring the energy landscape, and >> exclude them from the final analysis (whatever this is). At least this is >> what I've seen doing in publications and this is what I have understood >> from our previous conversations. I think your objection is about the way I >> use the term "equilibration" to refer to what you call "relaxation" (I >> presume it is not the same as energy minimization). Perhaps it would be >> helpful to have your definition of the terms "equilibration" and >> "relaxation. >> >> >> > equilibration from that is blatantly fooling yourself. >> > If you feel you must use cosine content to support any claim on >> > equilibration, then it is a much better approach to start from the end >> > of the simulation and check that the stretch of the trajectory you >> > take does not yield high cosine contents, in which case you have some >> > reason to argue that that part of the simulation is sampled in a local >> > equilibrium. >> > >> > Cheers, >> > >> > Tsjerk >> > >> > >> > On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis >> > wrote: >> > > You don't do it the right way. You must start the analysis from the >> > > beginning not from the end of your trajectory. I.e. >> > > >> > > 0-20ns >> > > 0-30ns >> > > 0-40ns >> > > ... >> > > 0-100ns >> > > >> > > Until the cosine content of the first 3 principal components that >> account >> > > for most of the variance in the atomic fluctuation have been dropped at >> > > least once below 0.5. This is the point where theoretically the system >> > has >> > > equilibrated enough. >> > > >> > > Thomas >> > > >> > > >> > > On 22 February 2013 13:43, Ahmet yıldırım wrote: >> > > >> > >> Dear users, >> > >> >> > >> I performed MD simulation of 400 ns of a structure. I used the cosine >> > >> content to check whether the simulation is not converged. I used last >> > 100 >> > >> and 50 ns of trajectory to the analysis, respectively. The results >> were >> > >> very similar to each other.The cosine contents of the first ten >> > principal >> > >> components are as follows. The cosine contents of the principal >> > components >> > >> are very small but one. Why is the second cosine content differs from >> > the >> > >> others? What could be the reason for this? And do you think simulation >> > has >> > >> reached convergence? >> > >> >> > >> The cosine contents of last 50 ns: >> > >> 1 0.00685769 >> > >> 2 0.137028 >> > >> 3 0.00139929 >> > >> 4 0.00903137 >> > >> 5 0.0180072 >> > >> 6 0.0128686 >> > >> 7 0.00154502 >> > >> 8 9.71793e-05 >> > >> 9 0.00485945 >> > >> 10 0.00202377 >> > >> >> > >> Thanks in advance >> > >> -- >> > >> Ahmet Yıldırım >> > >> -- >> > >> 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 >> > >> >> > > >> > > >> > > >> > > -- >> > > >> > > == >> > > >> > > Thomas Evangelidis >> > > >> > > PhD student >> > > University of Athens >> > > Faculty of Pharmacy >> > > Department of Pharmaceutical Chemistry >> > > Panepistimioupoli-Zografou >> > > 157 71 Athens >> > > GREECE >> > > >> > > email: tev...@pharm.uoa.gr >> > > >> > > teva...@gmail.com >> > > >> > > >> > > website: https://sites.google.com/site/thomasevangelidishomepage/ >> > > -- >> > > 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] Building a box pure solvent with genbox for CG simulations
Hello All, It is a newbie question here, but I can not find a clear response. I would like to create a simple box of pure DECANE for MD with the Martini force field. I have tried do that with genbox (as for AA force field) genbox_mpi -cp 1_CG_DECANE.pdb -ci 1_CG_DECANE.pdb -o CG_DECANE_box.gro -box 4.8 4.8 4.8 -nmol 255 -vdwd 0.21 where 1_CG_DECANE.pdb file contains three atoms (or beads) for decane. This atoms C1, C2 and C3 are placed according the geometry given in the martini_v2.0_solvents.itp file (i.e distance between beads of 4.7 A and angle of 180o). With this command, only the first atom of the DEC molecule is added in the box. So how to construct of pure solvent when i use the Martini force field In addition i have tried to use the martinize python script to transform a box of decane (AA) -> CG, but seemes to work only for proteins (correct ?). Thank you in advance for your help Stephane -- 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] Building a box pure solvent with genbox for CG simulations
Hi Stephane, martinize.py was written to convert proteins. But you can just take C2+C5+C8 from atomistic decane and energy minimize against the martini topology and you'll be fine. Cheers, Tsjerk On Mon, Feb 25, 2013 at 1:39 PM, ABEL Stephane 175950 wrote: > Hello All, > > It is a newbie question here, but I can not find a clear response. I would > like to create a simple box of pure DECANE for MD with the Martini force > field. I have tried do that with genbox (as for AA force field) > > genbox_mpi -cp 1_CG_DECANE.pdb -ci 1_CG_DECANE.pdb -o CG_DECANE_box.gro -box > 4.8 4.8 4.8 -nmol 255 -vdwd 0.21 > > where 1_CG_DECANE.pdb file contains three atoms (or beads) for decane. This > atoms C1, C2 and C3 are placed according the geometry given in the > martini_v2.0_solvents.itp file (i.e distance between beads of 4.7 A and angle > of 180o). With this command, only the first atom of the DEC molecule is added > in the box. > > So how to construct of pure solvent when i use the Martini force field > > In addition i have tried to use the martinize python script to transform a > box of decane (AA) -> CG, but seemes to work only for proteins (correct ?). > > Thank you in advance for your help > > Stephane > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: AW: AW: [gmx-users] g_current
Hello, I am using Gromacs VERSION 4.0.7. Nilesh > Hi, > > Which version of gromacs are you using. I am applying this tool also to > ILs > and it works fine for me in the release-4-5 branch. It is especially > strange > that you have a rotational dipole moment of zero. However, currently I > have > no idea where the segfault arises. Especially because you get an output. > So > what version you are using? > > Cheers, > Flo > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> Gesendet: Montag, 25. Februar 2013 00:05 >> An: Discussion list for GROMACS users >> Betreff: Re: AW: [gmx-users] g_current >> >> Hello, >> >> My system is ionic liquids composed of 128 cation (EMIM) and 128 anion > (ethyl >> sulfate). I choose system (0) as index group. >> >> Nilesh >> >> > Hi, >> > >> > Can you be a little bit more specific about your system, and what you >> > have chosen as index groups ? >> > >> > /Flo >> > >> > --- >> > Florian Dommert >> > Dipl. Phys. >> > >> > Institut für Computerphysik >> > Universität Stuttgart >> > Allmandring 3 >> > D-70569 Stuttgart >> > >> > Tel.: 0711-68563613 >> > Fax: 0711-68563658 >> > >> >> -Ursprüngliche Nachricht- >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> Gesendet: Samstag, 23. Februar 2013 16:17 >> >> An: gmx-users@gromacs.org >> >> Betreff: [gmx-users] g_current >> >> >> >> Hello, >> >> >> >> I am calculating the correlation of the rotational and translational >> > dipole >> >> moment of the system using g_current. >> >> >> >> I used following command >> >> >> >> g_current -f md.trr -s md.tpr mc >> >> >> >> It crashed with segmental fault. >> >> Last frame 15000 time 3.002 >> >> Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11 >> >> >> >> >> >> Average translational dipole moment M_J [enm] after 15001 frames >> >> (|M|^2): >> >> -0.00 -0.00 -0.00 (0.00) >> >> >> >> >> >> Average molecular dipole moment M_D [enm] after 15001 frames (|M|^2): >> >> -7.281919 17.954138 5.845435 (490.493744) >> >> >> >> >> >> >> >> Absolute values: >> >> epsilon=2723.718750 >> >> , , <(M_J*M_D)^2>: (490.493744, 0.00, -0.03) >> >> >> >> >> >> >> >> >> >> Fluctuations: >> >> epsilon=450.336090 >> >> >> >> >> >> deltaM_D , deltaM_J, deltaM_JD: (80.947235, 0.00, 0.00) >> >> >> >> >> >> >> >> Static dielectric constant using integral and fluctuations: >> >> 450.336090 >> >> >> >> < M_JM_D > via integral: -0.000 >> >> >> >> *** >> >> >> >> Average volume V=42.031509 nm^3 at T=300.00 K and corresponding >> >> refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975 >> >> >> >> Start fit at 98.08 ps (100.00). >> >> End fit at 398.31 ps (400.00). >> >> >> >> Einstein-Helfand fit to the MSD of the translational dipole moment >> >> yields: >> >> >> >> sigma=0. >> >> translational fraction of M^2: 0. Dielectric constant using EH: >> >> 2723.7188 Segmentation fault >> >> >> >> >> >> Can you whats the problem? >> >> >> >> Nilesh >> >> >> >> -- >> >> gmx-users mailing listgmx-users@gromacs.org >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >> * Please don't post (un)subscribe requests to the list. Use the www >> > interface or >> >> send it to gmx-users-requ...@gromacs.org. >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > -- >> > gmx-users mailing listgmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > * Please don't post (un)subscribe requests to the list. Use the www >> > interface or send it to gmx-users-requ...@gromacs.org. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the www > interface or >> send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http:
Re: [gmx-users] Error during npt equilibration in coarse grained simulation
On 2/25/13 12:16 AM, Anu Chandran wrote: Dear users, I am trying to do a coarse grained simulation of an octamer of a 350 residue protein in water using gromacs-4.5.3 using martini force field. I got the following error when i started running NPT equilibration "Step 32, time 0.64 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 16.561310, max 137.568573 (between atoms 626 and 627) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 32, time 0.64 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 438.087891, max 3717.233887 (between atoms 580 and 581) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 626627 121.90.2705 36.7207 0.2650 621622 90.00.2756 0.4600 0.2700 624626 91.50.3368 269.7515 0.3300 621623 90.00.2756 0.3172 0.2700 620624 90.40.3164 432.6003 0.3100 622623 90.00.2756 0.3991 0.2700 618620 85.50.3164 477.1006 0.3100 626627 121.90.2705 36.7206 0.2650 615618 88.60.3164 211.2461 0.3100 607610 141.30.3164 14.3253 0.3100 Step 32, time 0.64 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 134.347206, max 2000.691284 (between atoms 4949 and 4946) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 610612 149.20.3164 17.6610 0.3100 612614 89.70.3164 3.1394 0.3100 614615 150.90.3164 9.9306 0.3100 615618 88.60.3164 211.1131 0.3100 618620 85.50.3164 477.0737 0.3100 620624 90.40.3164 432.5994 0.3100 4950 4949 75.80.3164 146.5132 0.3100 624626 91.50.3368 269.7514 0.3300 4952 4950 118.90.3164 14.6303 0.3100 468469 90.00.2705 24.6834 0.2650 4941 4939 90.00.3368 8.5601 0.3300 585586 61.30.2756 0.3361 0.2700 4944 4941 82.50.3164 206.9830 0.3100 586587 90.10.2756 0.3137 0.2700 4946 4944 90.00.3164 583.5660 0.3100 606607 90.00.3368 6.6314 0.3300 4949 4946 90.00.3164 620.5243 0.3100 580581 91.90.4030 1003.9232 0.2700 4954 4952 90.30.3164 1.6571 0.3100 580582 89.80.2756 960.9988 0.2700 582583 98.60.2756 592.0677 0.2700 463464 90.00.2654 7.6858 0.2600 581582 88.80.1280 193.0707 0.2700 581583 91.30.2254 514.1149 0.2700 Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault (core dumped)" Energy minimization and the NVT equilibration ran without any error or warning. The mdp file used is as shown below; title= Martini define = -DPOSRES integrator = md dt = 0.02 nsteps = 5 nstcomm = 10 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 100 nstxtcout= 1000 xtc_precision= 100 xtc-grps = energygrps = Protein W nstlist = 10 ns_type = grid pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r= 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = System tau_t= 1.0 ref_t= 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p= 5.0 compressibility = 3e-4 ref_p= 1.0 gen_vel = yes If you ran NVT previously, regenerating velocities defeats that purpose and perturbs the system unnecessarily. Further, Parrinello-Rahman is not very stable for initial equilibration; use Berendsen and then switch to P-R for data collection. gen_temp = 300 gen_seed = 473529 constraints = none constraint_algorithm = Lincs unconstrained_start = no lincs_order = 4 lincs_warnangle = 30 Also the water box after energy minimization showed some gaps towards the edge of the box when visualized using VMD. can anybody please help me on how to overcome this error? In addition to the above, see the standard advice for unstable s
Re: [gmx-users] Simulation problem
On 2/25/13 1:01 AM, Jernej Zidar wrote: Hi. I've been running some polymer simulations on our cluster and I'm getting this error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. What does this error mean? I imagine it is somehow related to the unit cell. Could the error be related to the fact that the unit cell is rather long (along x axis) but short along the other axis. The thickness of the solvation layer is 2.0 nm, which should be OK. The error means that fluctuation of the unit cell dimensions will cause violation of the minimum image convention. Either the simulation box has become unstable and is going to crash, or you have larger fluctuations than you anticipated in the pressure (and thus box size) when building the system. -Justin I use the following input: ; Run parameters integrator = md; leap-frog integrator nsteps = 2500 ; 2 * 2500 = 50 ns dt = 0.002 ; 2 fs ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm= lincs ; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Output control nstxout = 1 ; save coordinates every 20 ps nstenergy = 1000 ; save energies every 20 ps nstlog = 1000 ; update log file every 20 ps ; Neighbour searching ns_type = grid nstlist = 5 rlist = 1.2 ; short-range neighborlist cutoff (in nm) ; Non-bonded interactions vdw-type= shift rvdw= 1.0 ; short-range van der Waals cutoff (in nm) rvdw-switch = 0.8 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT optimize-fft= yes ; optimize the FFT transforms for the current problem ; Temperature coupling is on for three groups tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = POLYMER Water_CL_NA ; three coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5; isothermal compressibility, bar^-1 ; Miscelanous gen_vel = no; Velocity generation is off dispcorr= no; account for cut-off vdW scheme ; Center of mass (COM) motion removal ; Reason: these options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 10 comm-mode = Linear comm-grps = POLYMER Water_CL_NA - - - Thanks in advance for any help or advice, Jernej Zidar -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] request
On 2/25/13 6:09 AM, Group Gro wrote: Dear Gromacs Users. I apologize for asking a question that has come up several times by numerous users in the previous e-mails, but I have read the answers and suggestions to those posts and I am not still able to solve the problem based on them. It is completely possible that I am just not seeing the obvious, so I apologize, but I would welcome any advice. I want to work on "Human Glutathione Peroxidase" and downloaded its pdb file, but when I try pdb2gmx, I face Fatal Error: Program pdb2gmx, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/pgutil.c, line: 91 Fatal error: Atom CD is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 50. I tried different force fields, for example OPLS-AA/L all-atom force field, different versions of AMBERs, but I always get the same problem! When I tried GROMOS's versions, the problem goes on CZ atom instead of CD. Here is a chunk of my pdb file (I have also attached the full pdb file to this e-mail): SHEET6 A 1 PHE A 183 PRO A190 0 SHEET7 A 1 GLY A 192 HIS A200 0 MODEL ATOM 1N GLY A 38 -4.242 -9.833 -26.316 1.00 0.00 N ATOM 2 CA GLY A 38 -3.416 -10.949 -25.765 1.00 0.00 C ATOM 3C GLY A 38 -1.953 -10.570 -25.632 1.00 0.00 C ATOM 4O GLY A 38 -1.069 -11.266 -26.159 1.00 0.00 O ATOM 5N THR A 39 -1.673 -9.461 -24.940 1.00 0.00 N ATOM 6 CA THR A 39 -0.286 -9.039 -24.705 1.00 0.00 C ATOM 7C THR A 39 -0.073 -8.722 -23.214 1.00 0.00 C ATOM 8O THR A 39 -1.035 -8.559 -22.442 1.00 0.00 O ATOM 9 CB THR A 39 0.124 -7.784 -25.533 1.00 0.00 C ATOM 10 OG1 THR A 39 -0.415 -6.602 -24.926 1.00 0.00 O ATOM 11 CG2 THR A 39 -0.309 -7.882 -27.037 1.00 0.00 C ….. ATOM 91 OD1 ASP A 49 10.106 1.841 -5.471 1.00 0.00 O ATOM 92 OD2 ASP A 49 12.010 2.918 -5.273 1.00 0.00 O ATOM 93N GLY A 50 8.192 0.495 -3.643 1.00 0.00 N ATOM 94 CA GLY A 50 6.805 0.919 -3.449 1.00 0.00 C ATOM 95C GLY A 50 6.525 2.278 -4.054 1.00 0.00 C ATOM 96O GLY A 50 5.449 2.818 -3.864 1.00 0.00 O ATOM 97N GLU A 51 7.471 2.832 -4.802 1.00 0.00 N ATOM 98 CA GLU A 51 7.351 4.238 -5.211 1.00 0.00 C ATOM 99C GLU A51 6.737 4.438 -6.592 1.00 0.00 C ATOM100O GLU A 51 6.291 5.522 -6.897 1.00 0.00 O ATOM101 CB GLU A 51 8.713 4.941 -5.174 1.00 0.00 C ATOM102 CG GLU A 51 9.283 5.140 -3.759 1.00 0.00 C ATOM103 CD GLU A 51 8.612 6.301 -3.006 1.00 0.00 C ATOM104N GLU A 52 6.729 3.418 -7.432 1.00 0.00 N …. ATOM3035OH TYR A 228 -9.320 -43.377 -52.577 1.00 0.00 O TER3036 TYR A 228 ENDMDL HETATM 3037 CL CL 11000 -16.070 -39.525 -6.168 1.00 0.00 CL HETATM 3038 NA NA 11001 -1.679 -34.065 -0.491 1.00 0.00 NA CONECT 996 1519 CONECT 1021 1519 CONECT 1519 996 1021 END I know that the residue number printed by pdb2gmx is actually starting from zero, so the problem is actually in GLU. In both rtp file and pdb I have CD atom. Some suggestions wanted to change the order of C and O in pdb file, but it didn't work. What should I do? Your statements are inconsistent. You say above that changing the force field triggers a problem with a different atom (CZ instead of CD), which doesn't make much sense. The amino acids have standard atom nomenclature, so changing the force field should not change the error. Beyond that, the real reason is that you're missing an atom somewhere and the PDB header should have clearing "MISSING" lines that tell you exactly what that is. If you need further help diagnosing, providing the actual PDB code would be helpful. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Dimer Dissociation Problem
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing the list and ask that further comments and questions will be posted there. On 2/25/13 7:42 AM, mrda...@gmail.com wrote: Dear Justin Greetings I simulate HIV-1 Protease with its substrate for 20ns in cubic box filled with SPC water using the following parameters: title = n.pdb cpp = /lib/cpp constraints = none integrator = md dt = 0.001 nsteps = 2000 nstcomm = 1 comm_mode = Linear comm_grps = nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb= 1.2 rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 tc-grps = system ref_t = 310 ; Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 310 K. gen_vel = yes gen_temp= 310.0 gen_seed= 173529 Unfortunately the dimer is dissociate to its monomers. what is the problem causing this unwanted event? thank you very much for your considerations I doubt it's actually dissociating. What you're seeing is probably a simple result of periodic boundary conditions. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions If a trajectory that has been properly post-processed by trjconv shows a dissociation event, then you should be able to easily observe why it happens by watching the trajectory in your favorite visualization software. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] regarding the cosine content analysis
Then, these cosine content's results are all normal? 2013/2/25 Tsjerk Wassenaar > Because it fits a little bit better to a cosine with full period than > the first one fits a cosine with half period and the third one fits a > cosine with 1.5 period. > > Tsjerk > > On Mon, Feb 25, 2013 at 1:23 PM, Ahmet yıldırım > wrote: > > Hi, > > > > I think my question was misunderstood. > > My question is: > > Why is second cosine content greater than the other values? > > > > Regards > > > > 2013/2/25 Thomas Evangelidis > > > >> On 25 February 2013 12:14, Tsjerk Wassenaar wrote: > >> > >> > Hi Thomas, > >> > > >> > As I've explained previously, the cosine content does not allow such > >> > inferences. Besides, taking the relaxation from the start into account > >> > in PCA is pretty nonsensical, unless you aim to characterize that > >> > relaxation in the first place. Looking at the cosine content to infer > >> > > >> > >> Yes, that's what I meant, to identity those ns where the protein does > >> unidirectional motion before it starts exploring the energy landscape, > and > >> exclude them from the final analysis (whatever this is). At least this > is > >> what I've seen doing in publications and this is what I have understood > >> from our previous conversations. I think your objection is about the > way I > >> use the term "equilibration" to refer to what you call "relaxation" (I > >> presume it is not the same as energy minimization). Perhaps it would be > >> helpful to have your definition of the terms "equilibration" and > >> "relaxation. > >> > >> > >> > equilibration from that is blatantly fooling yourself. > >> > If you feel you must use cosine content to support any claim on > >> > equilibration, then it is a much better approach to start from the end > >> > of the simulation and check that the stretch of the trajectory you > >> > take does not yield high cosine contents, in which case you have some > >> > reason to argue that that part of the simulation is sampled in a local > >> > equilibrium. > >> > > >> > Cheers, > >> > > >> > Tsjerk > >> > > >> > > >> > On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis < > teva...@gmail.com> > >> > wrote: > >> > > You don't do it the right way. You must start the analysis from the > >> > > beginning not from the end of your trajectory. I.e. > >> > > > >> > > 0-20ns > >> > > 0-30ns > >> > > 0-40ns > >> > > ... > >> > > 0-100ns > >> > > > >> > > Until the cosine content of the first 3 principal components that > >> account > >> > > for most of the variance in the atomic fluctuation have been > dropped at > >> > > least once below 0.5. This is the point where theoretically the > system > >> > has > >> > > equilibrated enough. > >> > > > >> > > Thomas > >> > > > >> > > > >> > > On 22 February 2013 13:43, Ahmet yıldırım > wrote: > >> > > > >> > >> Dear users, > >> > >> > >> > >> I performed MD simulation of 400 ns of a structure. I used the > cosine > >> > >> content to check whether the simulation is not converged. I used > last > >> > 100 > >> > >> and 50 ns of trajectory to the analysis, respectively. The results > >> were > >> > >> very similar to each other.The cosine contents of the first ten > >> > principal > >> > >> components are as follows. The cosine contents of the principal > >> > components > >> > >> are very small but one. Why is the second cosine content differs > from > >> > the > >> > >> others? What could be the reason for this? And do you think > simulation > >> > has > >> > >> reached convergence? > >> > >> > >> > >> The cosine contents of last 50 ns: > >> > >> 1 0.00685769 > >> > >> 2 0.137028 > >> > >> 3 0.00139929 > >> > >> 4 0.00903137 > >> > >> 5 0.0180072 > >> > >> 6 0.0128686 > >> > >> 7 0.00154502 > >> > >> 8 9.71793e-05 > >> > >> 9 0.00485945 > >> > >> 10 0.00202377 > >> > >> > >> > >> Thanks in advance > >> > >> -- > >> > >> Ahmet Yıldırım > >> > >> -- > >> > >> 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 > >> > >> > >> > > > >> > > > >> > > > >> > > -- > >> > > > >> > > > == > >> > > > >> > > Thomas Evangelidis > >> > > > >> > > PhD student > >> > > University of Athens > >> > > Faculty of Pharmacy > >> > > Department of Pharmaceutical Chemistry > >> > > Panepistimioupoli-Zografou > >> > > 157 71 Athens > >> > > GREECE > >> > > > >> > > email: tev...@pharm.uoa.gr > >> > > > >> > > teva...@gmail.com > >> > > > >> > > > >> > > website: https://sites.google.com/site/thomasevangelidishomepage/ > >> > > -- > >> > > gmx-users mailing listgmx-users@groma
Re: [gmx-users] regarding the cosine content analysis
Well, the cosine content doesn't tell you very much anyway. And fitting a cosine with a full period to the second component only makes sense if the first fits well to a half cosine. If the correlation coefficient is about .1, it tells you less. It says nothing, absolutely nothing about convergence and/or equilibrium. Cheers, Tsjerk On Mon, Feb 25, 2013 at 2:36 PM, Ahmet yıldırım wrote: > Then, these cosine content's results are all normal? > > 2013/2/25 Tsjerk Wassenaar > >> Because it fits a little bit better to a cosine with full period than >> the first one fits a cosine with half period and the third one fits a >> cosine with 1.5 period. >> >> Tsjerk >> >> On Mon, Feb 25, 2013 at 1:23 PM, Ahmet yıldırım >> wrote: >> > Hi, >> > >> > I think my question was misunderstood. >> > My question is: >> > Why is second cosine content greater than the other values? >> > >> > Regards >> > >> > 2013/2/25 Thomas Evangelidis >> > >> >> On 25 February 2013 12:14, Tsjerk Wassenaar wrote: >> >> >> >> > Hi Thomas, >> >> > >> >> > As I've explained previously, the cosine content does not allow such >> >> > inferences. Besides, taking the relaxation from the start into account >> >> > in PCA is pretty nonsensical, unless you aim to characterize that >> >> > relaxation in the first place. Looking at the cosine content to infer >> >> > >> >> >> >> Yes, that's what I meant, to identity those ns where the protein does >> >> unidirectional motion before it starts exploring the energy landscape, >> and >> >> exclude them from the final analysis (whatever this is). At least this >> is >> >> what I've seen doing in publications and this is what I have understood >> >> from our previous conversations. I think your objection is about the >> way I >> >> use the term "equilibration" to refer to what you call "relaxation" (I >> >> presume it is not the same as energy minimization). Perhaps it would be >> >> helpful to have your definition of the terms "equilibration" and >> >> "relaxation. >> >> >> >> >> >> > equilibration from that is blatantly fooling yourself. >> >> > If you feel you must use cosine content to support any claim on >> >> > equilibration, then it is a much better approach to start from the end >> >> > of the simulation and check that the stretch of the trajectory you >> >> > take does not yield high cosine contents, in which case you have some >> >> > reason to argue that that part of the simulation is sampled in a local >> >> > equilibrium. >> >> > >> >> > Cheers, >> >> > >> >> > Tsjerk >> >> > >> >> > >> >> > On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis < >> teva...@gmail.com> >> >> > wrote: >> >> > > You don't do it the right way. You must start the analysis from the >> >> > > beginning not from the end of your trajectory. I.e. >> >> > > >> >> > > 0-20ns >> >> > > 0-30ns >> >> > > 0-40ns >> >> > > ... >> >> > > 0-100ns >> >> > > >> >> > > Until the cosine content of the first 3 principal components that >> >> account >> >> > > for most of the variance in the atomic fluctuation have been >> dropped at >> >> > > least once below 0.5. This is the point where theoretically the >> system >> >> > has >> >> > > equilibrated enough. >> >> > > >> >> > > Thomas >> >> > > >> >> > > >> >> > > On 22 February 2013 13:43, Ahmet yıldırım >> wrote: >> >> > > >> >> > >> Dear users, >> >> > >> >> >> > >> I performed MD simulation of 400 ns of a structure. I used the >> cosine >> >> > >> content to check whether the simulation is not converged. I used >> last >> >> > 100 >> >> > >> and 50 ns of trajectory to the analysis, respectively. The results >> >> were >> >> > >> very similar to each other.The cosine contents of the first ten >> >> > principal >> >> > >> components are as follows. The cosine contents of the principal >> >> > components >> >> > >> are very small but one. Why is the second cosine content differs >> from >> >> > the >> >> > >> others? What could be the reason for this? And do you think >> simulation >> >> > has >> >> > >> reached convergence? >> >> > >> >> >> > >> The cosine contents of last 50 ns: >> >> > >> 1 0.00685769 >> >> > >> 2 0.137028 >> >> > >> 3 0.00139929 >> >> > >> 4 0.00903137 >> >> > >> 5 0.0180072 >> >> > >> 6 0.0128686 >> >> > >> 7 0.00154502 >> >> > >> 8 9.71793e-05 >> >> > >> 9 0.00485945 >> >> > >> 10 0.00202377 >> >> > >> >> >> > >> Thanks in advance >> >> > >> -- >> >> > >> Ahmet Yıldırım >> >> > >> -- >> >> > >> gmx-users mailing listgmx-users@gromacs.org >> >> > >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> > >> * Please search the archive at >> >> > >> http://www.gromacs.org/Support/Mailing_Lists/Search before >> posting! >> >> > >> * Please don't post (un)subscribe requests to the list. Use the >> >> > >> www interface or send it to gmx-users-requ...@gromacs.org. >> >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > >> >> >> > > >> >> > > >> >> > > >> >> > > -- >> >> > > >> >> > > >>
AW: AW: AW: [gmx-users] g_current
Hi, Can you update your Gromacs version to an actual release and check if the problem still occurs. It is very strange that the Einstein-Helfand fit gives 0 for sigma and M_J^2. Cheers, Flo --- Florian Dommert Dipl. Phys. Institut für Computerphysik Universität Stuttgart Allmandring 3 D-70569 Stuttgart Tel.: 0711-68563613 Fax: 0711-68563658 > -Ursprüngliche Nachricht- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > Gesendet: Montag, 25. Februar 2013 14:00 > An: Discussion list for GROMACS users > Betreff: Re: AW: AW: [gmx-users] g_current > > Hello, > > I am using Gromacs VERSION 4.0.7. > > Nilesh > > > > Hi, > > > > Which version of gromacs are you using. I am applying this tool also > > to ILs and it works fine for me in the release-4-5 branch. It is > > especially strange that you have a rotational dipole moment of zero. > > However, currently I have no idea where the segfault arises. > > Especially because you get an output. > > So > > what version you are using? > > > > Cheers, > > Flo > > > >> -Ursprüngliche Nachricht- > >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > >> Gesendet: Montag, 25. Februar 2013 00:05 > >> An: Discussion list for GROMACS users > >> Betreff: Re: AW: [gmx-users] g_current > >> > >> Hello, > >> > >> My system is ionic liquids composed of 128 cation (EMIM) and 128 > >> anion > > (ethyl > >> sulfate). I choose system (0) as index group. > >> > >> Nilesh > >> > >> > Hi, > >> > > >> > Can you be a little bit more specific about your system, and what > >> > you have chosen as index groups ? > >> > > >> > /Flo > >> > > >> > --- > >> > Florian Dommert > >> > Dipl. Phys. > >> > > >> > Institut für Computerphysik > >> > Universität Stuttgart > >> > Allmandring 3 > >> > D-70569 Stuttgart > >> > > >> > Tel.: 0711-68563613 > >> > Fax: 0711-68563658 > >> > > >> >> -Ursprüngliche Nachricht- > >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal > >> >> Gesendet: Samstag, 23. Februar 2013 16:17 > >> >> An: gmx-users@gromacs.org > >> >> Betreff: [gmx-users] g_current > >> >> > >> >> Hello, > >> >> > >> >> I am calculating the correlation of the rotational and > >> >> translational > >> > dipole > >> >> moment of the system using g_current. > >> >> > >> >> I used following command > >> >> > >> >> g_current -f md.trr -s md.tpr mc > >> >> > >> >> It crashed with segmental fault. > >> >> Last frame 15000 time 3.002 > >> >> Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11 > >> >> > >> >> > >> >> Average translational dipole moment M_J [enm] after 15001 frames > >> >> (|M|^2): > >> >> -0.00 -0.00 -0.00 (0.00) > >> >> > >> >> > >> >> Average molecular dipole moment M_D [enm] after 15001 frames > (|M|^2): > >> >> -7.281919 17.954138 5.845435 (490.493744) > >> >> > >> >> > >> >> > >> >> Absolute values: > >> >> epsilon=2723.718750 > >> >> , , <(M_J*M_D)^2>: (490.493744, 0.00, > >> >> -0.03) > >> >> > >> >> > >> >> > >> >> > >> >> Fluctuations: > >> >> epsilon=450.336090 > >> >> > >> >> > >> >> deltaM_D , deltaM_J, deltaM_JD: (80.947235, 0.00, 0.00) > >> >> > >> >> > >> >> > >> >> Static dielectric constant using integral and fluctuations: > >> >> 450.336090 > >> >> > >> >> < M_JM_D > via integral: -0.000 > >> >> > >> >> *** > >> >> > >> >> Average volume V=42.031509 nm^3 at T=300.00 K and > >> >> corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975 > >> >> > >> >> Start fit at 98.08 ps (100.00). > >> >> End fit at 398.31 ps (400.00). > >> >> > >> >> Einstein-Helfand fit to the MSD of the translational dipole moment > >> >> yields: > >> >> > >> >> sigma=0. > >> >> translational fraction of M^2: 0. Dielectric constant using EH: > >> >> 2723.7188 Segmentation fault > >> >> > >> >> > >> >> Can you whats the problem? > >> >> > >> >> Nilesh > >> >> > >> >> -- > >> >> 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.
Re: AW: AW: AW: [gmx-users] g_current
Hello, Thanks. I will update Gromacs version. Can you tell which version you are using ? Nilesh > Hi, > > Can you update your Gromacs version to an actual release and check if the > problem still occurs. It is very strange that the Einstein-Helfand fit > gives > 0 for sigma and M_J^2. > > Cheers, > Flo > > --- > Florian Dommert > Dipl. Phys. > > Institut für Computerphysik > Universität Stuttgart > Allmandring 3 > D-70569 Stuttgart > > Tel.: 0711-68563613 > Fax: 0711-68563658 > >> -Ursprüngliche Nachricht- >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> Gesendet: Montag, 25. Februar 2013 14:00 >> An: Discussion list for GROMACS users >> Betreff: Re: AW: AW: [gmx-users] g_current >> >> Hello, >> >> I am using Gromacs VERSION 4.0.7. >> >> Nilesh >> >> >> > Hi, >> > >> > Which version of gromacs are you using. I am applying this tool also >> > to ILs and it works fine for me in the release-4-5 branch. It is >> > especially strange that you have a rotational dipole moment of zero. >> > However, currently I have no idea where the segfault arises. >> > Especially because you get an output. >> > So >> > what version you are using? >> > >> > Cheers, >> > Flo >> > >> >> -Ursprüngliche Nachricht- >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> Gesendet: Montag, 25. Februar 2013 00:05 >> >> An: Discussion list for GROMACS users >> >> Betreff: Re: AW: [gmx-users] g_current >> >> >> >> Hello, >> >> >> >> My system is ionic liquids composed of 128 cation (EMIM) and 128 >> >> anion >> > (ethyl >> >> sulfate). I choose system (0) as index group. >> >> >> >> Nilesh >> >> >> >> > Hi, >> >> > >> >> > Can you be a little bit more specific about your system, and what >> >> > you have chosen as index groups ? >> >> > >> >> > /Flo >> >> > >> >> > --- >> >> > Florian Dommert >> >> > Dipl. Phys. >> >> > >> >> > Institut für Computerphysik >> >> > Universität Stuttgart >> >> > Allmandring 3 >> >> > D-70569 Stuttgart >> >> > >> >> > Tel.: 0711-68563613 >> >> > Fax: 0711-68563658 >> >> > >> >> >> -Ursprüngliche Nachricht- >> >> >> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> >> >> boun...@gromacs.org] Im Auftrag von Nilesh Dhumal >> >> >> Gesendet: Samstag, 23. Februar 2013 16:17 >> >> >> An: gmx-users@gromacs.org >> >> >> Betreff: [gmx-users] g_current >> >> >> >> >> >> Hello, >> >> >> >> >> >> I am calculating the correlation of the rotational and >> >> >> translational >> >> > dipole >> >> >> moment of the system using g_current. >> >> >> >> >> >> I used following command >> >> >> >> >> >> g_current -f md.trr -s md.tpr mc >> >> >> >> >> >> It crashed with segmental fault. >> >> >> Last frame 15000 time 3.002 >> >> >> Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11 >> >> >> >> >> >> >> >> >> Average translational dipole moment M_J [enm] after 15001 frames >> >> >> (|M|^2): >> >> >> -0.00 -0.00 -0.00 (0.00) >> >> >> >> >> >> >> >> >> Average molecular dipole moment M_D [enm] after 15001 frames >> (|M|^2): >> >> >> -7.281919 17.954138 5.845435 (490.493744) >> >> >> >> >> >> >> >> >> >> >> >> Absolute values: >> >> >> epsilon=2723.718750 >> >> >> , , <(M_J*M_D)^2>: (490.493744, 0.00, >> >> >> -0.03) >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Fluctuations: >> >> >> epsilon=450.336090 >> >> >> >> >> >> >> >> >> deltaM_D , deltaM_J, deltaM_JD: (80.947235, 0.00, 0.00) >> >> >> >> >> >> >> >> >> >> >> >> Static dielectric constant using integral and fluctuations: >> >> >> 450.336090 >> >> >> >> >> >> < M_JM_D > via integral: -0.000 >> >> >> >> >> >> *** >> >> >> >> >> >> Average volume V=42.031509 nm^3 at T=300.00 K and >> >> >> corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975 >> >> >> >> >> >> Start fit at 98.08 ps (100.00). >> >> >> End fit at 398.31 ps (400.00). >> >> >> >> >> >> Einstein-Helfand fit to the MSD of the translational dipole moment >> >> >> yields: >> >> >> >> >> >> sigma=0. >> >> >> translational fraction of M^2: 0. Dielectric constant using >> EH: >> >> >> 2723.7188 Segmentation fault >> >> >> >> >> >> >> >> >> Can you whats the problem? >> >> >> >> >> >> Nilesh >> >> >> >> >> >> -- >> >> >> 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: Building a box pure solvent with genbox for CG simulations
Many Thanks Tsjerk, It works A bientot Stephane -- Message: 3 Date: Mon, 25 Feb 2013 13:51:53 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Building a box pure solvent with genbox for CG simulations To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=UTF-8 Hi Stephane, martinize.py was written to convert proteins. But you can just take C2+C5+C8 from atomistic decane and energy minimize against the martini topology and you'll be fine. Cheers, Tsjerk On Mon, Feb 25, 2013 at 1:39 PM, ABEL Stephane 175950 wrote: > Hello All, > > It is a newbie question here, but I can not find a clear response. I would > like to create a simple box of pure DECANE for MD with the Martini force > field. I have tried do that with genbox (as for AA force field) > > genbox_mpi -cp 1_CG_DECANE.pdb -ci 1_CG_DECANE.pdb -o CG_DECANE_box.gro -box > 4.8 4.8 4.8 -nmol 255 -vdwd 0.21 > > where 1_CG_DECANE.pdb file contains three atoms (or beads) for decane. This > atoms C1, C2 and C3 are placed according the geometry given in the > martini_v2.0_solvents.itp file (i.e distance between beads of 4.7 A and angle > of 180o). With this command, only the first atom of the DEC molecule is added > in the box. > > So how to construct of pure solvent when i use the Martini force field > > In addition i have tried to use the martinize python script to transform a > box of decane (AA) -> CG, but seemes to work only for proteins (correct ?). > > Thank you in advance for your help > > Stephane > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Regarding Gromacs error
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing the list and ask that further comments and questions will be posted there. On 2/25/13 9:09 AM, bhavaniprasad vipperla wrote: Hello sir, I have been using GROMACS for my MD work. I had many queries cleared by you earlier. I got a query, please help me out regarding this. I am trying to do MD study for a phosphorylated and un-phosphorylated form of my protein. I have tried adding the phosphate group using Discovery studio but it doesn't get read as Phosphotyrosine while running in gromacs. I had obtained the modified forcefields submitted by you, having Phosphorylated versions of the Aminoacids from the gromacs website and using it for simulations. Its giving an error Warning: Residue PTR208 in chain has different type(other) from starting residue MET1 (Protein) Identified Residue ASN207 as a ending terminus. The above warnings are fixed by following step 5 here: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue *Fatal Error:* *Residue 'HISE' not found in residue topology database.* * * But i dont have any HISE residue in my topology and its also not reading the phosphorylated residue at 208 position. I tried checking in the gromacs forum, but couldnt find any related queries. So am asking for your help. Here, you probably need to add an entry in aminoacids.r2b to translate building block and .rtp names. HISE is the epsilon-protonated form of histidine, which is called HISB in many force fields. See existing force field files for an example. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] latest Gromacs paper
We are pleased to announce the publication last month of the latest Gromacs paper: GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson. Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl http://bioinformatics.oxfordjournals.org/content/early/2013/02/21/bioinformatics.btt055.abstract Thanks to everyone whose hard work made this possible. We hope you will find the paper interesting and informative. And yes, the paper version lags the software release version somewhat. -- 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: Gromacs 4.6 Installation under Cygwin
Hello, Thanks for the help. After setting the library path properly, I seem to be able to get gromacs up and running. However, I have run into another problem with mdrun and actually running any jobs. When I execute mdrun -v -deffnm Clp_Test -nt The output is: Reading file Clp_Test.tpr, VERSION 4.6 (single precision) Using 8 MPI threads Followed by several occurrences of: Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. Then: starting mdrun 'Martini system for ClpX' 1 steps,200.0 ps. After this however, the simulation never actually begins. I can get rid of the error messages by using -pin off, but that doesn't seem to actually fix anything. Is there something that has not been installed properly? Below is the seemingly relevant portions of the log file generated by the above mdrun command. Log file opened on Mon Feb 25 11:21:08 2013 Host: Theory-Monster pid: 3192 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6 Precision: single Memory model: 32 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.3-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Mon, Feb 25, 2013 10:38:04 AM Built by: Mike@Theory-Monster [CMAKE] Build OS/arch: CYGWIN_NT-6.1-WOW64 1.7.17(0.262/5/3) i686 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc.exe GNU gcc (GCC) 4.5.3 C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.988 nm, Bond, atoms 997 1005 multi-body bonded interactions: 1.042 nm, G96Angle, atoms 1938 1942 Minimum cell size due to bonded interactions: 1.146 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.810 nm Estimated maximum distance required for P-LINCS: 0.810 nm Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.433 nm The maximum allowed number of cells is: X 11 Y 11 Z 9 Domain decomposition grid 4 x 2 x 1, separate PME nodes 0 Domain decomposition nodeid 0, coordinates 0 0 0 Using 8 MPI threads Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.4 Coulomb: 1.2 LJ: 1.2 System total charge: 0.000 Generated table with 1200 data points for Shift. Tabscale = 500 points/nm Generated table with 1200 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1200 data points for LJ12Shift. Tabscale = 500 points/nm Potential shift: LJ r^-12: 0.000 r^-6 0.000 Removing pbc first time Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. Initializing Parallel LINear Constraint Solver PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 --- Thank You --- The number of constraints is 840 There are inter charge-group constraints, will communicate selected coordinates each lincs iteration 414 constraints are involved in constraint triangles, will apply an additional matrix expansion of order 4 for couplings between constraints inside triangles Linking all bonded interactions to atoms The initial number of communication pulses is: X 1 Y 1 The initial domain decomposition cell size is: X 4.02 nm Y 8.04 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded inter
[gmx-users] latest Gromacs paper
Dear Gromacs users, We are pleased to announce the publication last month of the latest Gromacs paper: GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson. Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl http://bioinformatics.oxfordjournals.org/content/early/2013/02/21/bioinformatics.btt055.abstract Thanks to everyone whose hard work made this possible. We hope you will find the paper interesting and informative. And yes, the paper version lags the software release version somewhat. -- 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] g_bar for larger systems (protein-protein interaction)
Hello dear users, I just took a look at the new gromacs paper at Bioinformatics, and I noticed a new tool g_bar, which is used for free energy calculations. I also found a nice tutorial by Justin Lemkul. While I'm adapting the workflow to my system, I'd like to know from anyone with more expertise in this field, if this method can be successfully applied to larger molecules as ligands, other than small organic ligands. What is the effectiveness in determining a protein-protein (300+ residues) energy of binding, if any? Thanks, Ricardo. -- 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] g_bar for larger systems (protein-protein interaction)
My personal opinion is that for large protein-protein calculations, the free energy should be computed through potential of mean force calculations, NOT alchemical methods, using the endpoints (properly corrected) to determine the free energy of association. There are a number of tutorials and example papers on how to compute these potentials of mean force, so I won't go into those details here. On Mon, Feb 25, 2013 at 3:49 PM, Ricardo O. S. Soares wrote: > Hello dear users, > > I just took a look at the new gromacs paper at Bioinformatics, and I noticed > a new tool g_bar, which is used for free energy calculations. I also found a > nice tutorial by Justin Lemkul. While I'm adapting the workflow to my > system, I'd like to know from anyone with more expertise in this field, if > this method can be successfully applied to larger molecules as ligands, > other than small organic ligands. What is the effectiveness in determining a > protein-protein (300+ residues) energy of binding, if any? > > Thanks, > > Ricardo. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Can not stop center of mass: maybe 2dimensional system
Hi, all gmx-users, I am trying to simulate a system of an ion restrained at the center of water cluster. So I set pbc = no, used "cut-off" for coulomb and vdw. To restrain the ion at the center of water cluster, I used COMM-pulling. Set water molecules and the ion in two groups, and applied distance pulling. Also, I set nstcomm = 10 comm_grps = system comm_mode = Angular, But the simulation stopped right after , and error is" Can not stop center of mass: maybe 2dimensional system". If I did not remove center of mass motion, the whole system drifted a lot and my system messed up. Could someone give me advices on how to solve this problem? thanks philip -- View this message in context: http://gromacs.5086.n6.nabble.com/Can-not-stop-center-of-mass-maybe-2dimensional-system-tp5005875.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin
That's strange, it seems that mdrun gets stuck somewhere. This should not happen, but as we don't actively test cygwin, we can't be sure what's happening. It would be great if you could help us figure out what is going wrong. Could you try doing the following: - run with -ntmpi 1 -ntomp 1 (i.e single-threaded); - run with OpenMP (-only) multhithreading, that is with -ntmpi 1 (this should start with 8 OpenMP threads) - run with -debug 1 which will produce the mdrun.debug output, please upload this to e.g pastebin and post a link; On a side-note: you would be better off using a newer gcc, 4.7 should be considerably faster than 4.5 - especially on this Sandy Bridge Xeon processor. Cheers, -- Szilárd On Mon, Feb 25, 2013 at 5:25 PM, wrote: > Hello, > Thanks for the help. After setting the library path properly, I seem > to be able to get gromacs up and running. However, I have run into another > problem with mdrun and actually running any jobs. When I execute > mdrun -v -deffnm Clp_Test -nt > The output is: Reading file Clp_Test.tpr, VERSION 4.6 (single precision) > Using 8 MPI threads > > Followed by several occurrences of: > Can not set thread affinities on the current platform. On NUMA systems this > can cause performance degradation. If you think your platform should > support > setting affinities, contact the GROMACS developers. > > Then: > starting mdrun 'Martini system for ClpX' > 1 steps,200.0 ps. > > After this however, the simulation never actually begins. I can get rid of > the error messages by using -pin off, but that doesn't seem to actually fix > anything. Is there something that has not been installed properly? Below is > the seemingly relevant portions of the log file generated by the above > mdrun command. > > > Log file opened on Mon Feb 25 11:21:08 2013 > Host: Theory-Monster pid: 3192 nodeid: 0 nnodes: 1 > Gromacs version:VERSION 4.6 > Precision: single > Memory model: 32 bit > MPI library:thread_mpi > OpenMP support: enabled > GPU support:disabled > invsqrt routine:gmx_software_invsqrt(x) > CPU acceleration: AVX_256 > FFT library:fftw-3.3.3-sse2 > Large file support: enabled > RDTSCP usage: enabled > Built on: Mon, Feb 25, 2013 10:38:04 AM > Built by: Mike@Theory-Monster [CMAKE] > Build OS/arch: CYGWIN_NT-6.1-WOW64 1.7.17(0.262/5/3) i686 > Build CPU vendor: GenuineIntel > Build CPU brand:Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz > Build CPU family: 6 Model: 45 Stepping: 7 > Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr > nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 > sse4.2 ssse3 tdt x2apic > C compiler: /usr/bin/gcc.exe GNU gcc (GCC) 4.5.3 > C compiler flags: -mavx -Wextra -Wno-missing-field-**initializers > -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer > -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG > > Initializing Domain Decomposition on 8 nodes > Dynamic load balancing: auto > Will sort the charge groups at every domain (re)decomposition > Initial maximum inter charge-group distances: >two-body bonded interactions: 0.988 nm, Bond, atoms 997 1005 > multi-body bonded interactions: 1.042 nm, G96Angle, atoms 1938 1942 > Minimum cell size due to bonded interactions: 1.146 nm > Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.810 nm > Estimated maximum distance required for P-LINCS: 0.810 nm > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 > Optimizing the DD grid for 8 cells with a minimum initial size of 1.433 nm > The maximum allowed number of cells is: X 11 Y 11 Z 9 > Domain decomposition grid 4 x 2 x 1, separate PME nodes 0 > Domain decomposition nodeid 0, coordinates 0 0 0 > > Using 8 MPI threads > > Detecting CPU-specific acceleration. > Present hardware specification: > Vendor: GenuineIntel > Brand: Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz > Family: 6 Model: 45 Stepping: 7 > Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc > pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 > tdt x2apic > Acceleration most likely to fit this hardware: AVX_256 > Acceleration selected at GROMACS compile time: AVX_256 > > Table routines are used for coulomb: TRUE > Table routines are used for vdw: TRUE > Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm > Cut-off's: NS: 1.4 Coulomb: 1.2 LJ: 1.2 > System total charge: 0.000 > Generated table with 1200 data points for Shift. > Tabscale = 500 points/nm > Generated table with 1200 data points for LJ6Shift. > Tabscale = 500 points/nm > Generated table with 1200 data points for LJ12Shift. > Tabscale = 500 points/nm > Potential shift: LJ r^-12: 0.000 r^-6 0.000 > Removing pbc first time > > Can not set thread affinities on the current platform. On NUMA systems this > can cause performance degradation. If you think your platfo
Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin
Hi, I have run the 3 scenarios that you mentioned. The commands and output are pasted below. Thanks, Mike ***Trial 1*** mdrun -v -deffnm Clp_Test -ntmpi 1 -ntomp 1 Reading file Clp_Test.tpr, VERSION 4.6 (single precision) Using 1 MPI thread Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. starting mdrun 'Martini system for ClpX' 1 steps,200.0 ps. --Relavant outpur from log file-- Log file opened on Mon Feb 25 20:26:57 2013 Host: Theory-Monster pid: 8176 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6 Precision: single Memory model: 32 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.3-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Mon, Feb 25, 2013 10:38:04 AM Built by: Mike@Theory-Monster [CMAKE] Build OS/arch: CYGWIN_NT-6.1-WOW64 1.7.17(0.262/5/3) i686 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 s se4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/gcc.exe GNU gcc (GCC) 4.5.3 C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG Using 1 MPI thread Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4 .2 ssse3 tdt x2apic Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 Table routines are used for coulomb: TRUE Table routines are used for vdw: TRUE Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm Cut-off's: NS: 1.4 Coulomb: 1.2 LJ: 1.2 System total charge: 0.000 Generated table with 1200 data points for Shift. Tabscale = 500 points/nm Generated table with 1200 data points for LJ6Shift. Tabscale = 500 points/nm Generated table with 1200 data points for LJ12Shift. Tabscale = 500 points/nm Potential shift: LJ r^-12: 0.000 r^-6 0.000 Removing pbc first time Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. Initializing LINear Constraint Solver PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 --- Thank You --- The number of constraints is 840 414 constraints are involved in constraint triangles, will apply an additional matrix expansion of order 4 for couplings between constraints inside triangles Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 (1984) pp. 3684-3690 --- Thank You --- ***Trial 2*** mdrun -v -deffnm Clp_Test -ntmpi 1 Reading file Clp_Test.tpr, VERSION 4.6 (single precision) Using 1 MPI thread Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. starting mdrun 'Martini system for ClpX' 1 steps,200.0 ps. --Relavant outpur from log file-- Log file opened on Mon Feb 25 20:40:32 2013 Host: Theory-Monster pid: 4624 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6 Precision: single Memory model: 32 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.3-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Mon, Feb 25, 2013 10:38:04 AM Built by: Mike@Theory-Monster [CMAKE] Build OS/arch: CYGWIN_NT-6.1-WOW64 1.7.17(0.262/5/3) i686 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt
[gmx-users] Output for rmsd and radius of gyration doubts
Hi, Just need some advice regarding the following results I obtained while following the tutorial from this site, using a protein structure that I modelled using Modeller. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ 1. My output plot of RMSD doesn't converge. (From 0 - 0.4ns, its around 0.25nm, 0.4 - 0.7, around 0.3nm, 0.7 - 1.0ns, around 0.35). Does it mean that my EM wasn't properly done? Anyway, the EM did not reach the requested Fmax <100. 2. My graph for Radius of gyration from 800 - 1000ps shows a higher fluctuation than the ones from 0 - 800ps. Does it mean that the structure is not that stable? Please advice. (I followed exactly the steps in that tutorial. I'm new to Gromacs.) And of course, I neutralized my protein according to the charge needed. Not exactly following blindly from the tutorial. ;) Thank you very much in advance! :) Best wishes. -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Output for rmsd and radius of gyration doubts
On 2/25/13 9:38 PM, Ewaru wrote: Hi, Just need some advice regarding the following results I obtained while following the tutorial from this site, using a protein structure that I modelled using Modeller. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ 1. My output plot of RMSD doesn't converge. (From 0 - 0.4ns, its around 0.25nm, 0.4 - 0.7, around 0.3nm, 0.7 - 1.0ns, around 0.35). Does it mean that my EM wasn't properly done? Anyway, the EM did not reach the requested Fmax <100. 2. My graph for Radius of gyration from 800 - 1000ps shows a higher fluctuation than the ones from 0 - 800ps. Does it mean that the structure is not that stable? Please advice. (I followed exactly the steps in that tutorial. I'm new to Gromacs.) And of course, I neutralized my protein according to the charge needed. Not exactly following blindly from the tutorial. ;) Please don't assume that 1 ns of MD for any system is actually meaningful, or that the results of some other protein will necessarily look anything like my example. The commands in the tutorial are just to show how one might go about doing analysis and demonstrating a few tools that can be used. Most protein systems require tens, if not hundreds, of ns to manifest the behavior of interest. The results you've posted indicate nothing more than the fact that your protein isn't yet anywhere close to equilibrium, which is not at all unexpected. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Output for rmsd and radius of gyration doubts
Dear Justin, Oh, no wonder. Thank you so much for your prompt reply! :) Best wishes. -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5005885.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error during npt equilibration in coarse grained simulation
Sir, I have tried Berendsen barostat for Pcoupl. Still I get the same error. Thank you, regards, Anu On Mon, Feb 25, 2013 at 6:58 PM, Justin Lemkul wrote: > > > On 2/25/13 12:16 AM, Anu Chandran wrote: > >> Dear users, >> I am trying to do a coarse grained simulation of an octamer of a 350 >> residue protein in water using gromacs-4.5.3 using martini force field. I >> got the following error when i started running NPT equilibration >> >> "Step 32, time 0.64 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 16.561310, max 137.568573 (between atoms 626 and 627) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> >> Step 32, time 0.64 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 438.087891, max 3717.233887 (between atoms 580 and 581) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 626627 121.90.2705 36.7207 0.2650 >> 621622 90.00.2756 0.4600 0.2700 >> 624626 91.50.3368 269.7515 0.3300 >> 621623 90.00.2756 0.3172 0.2700 >> 620624 90.40.3164 432.6003 0.3100 >> 622623 90.00.2756 0.3991 0.2700 >> 618620 85.50.3164 477.1006 0.3100 >> 626627 121.90.2705 36.7206 0.2650 >> 615618 88.60.3164 211.2461 0.3100 >> 607610 141.30.3164 14.3253 0.3100 >> >> Step 32, time 0.64 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 134.347206, max 2000.691284 (between atoms 4949 and 4946) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 610612 149.20.3164 17.6610 0.3100 >> 612614 89.70.3164 3.1394 0.3100 >> 614615 150.90.3164 9.9306 0.3100 >> 615618 88.60.3164 211.1131 0.3100 >> 618620 85.50.3164 477.0737 0.3100 >> 620624 90.40.3164 432.5994 0.3100 >> 4950 4949 75.80.3164 146.5132 0.3100 >> 624626 91.50.3368 269.7514 0.3300 >> 4952 4950 118.90.3164 14.6303 0.3100 >> 468469 90.00.2705 24.6834 0.2650 >> 4941 4939 90.00.3368 8.5601 0.3300 >> 585586 61.30.2756 0.3361 0.2700 >> 4944 4941 82.50.3164 206.9830 0.3100 >> 586587 90.10.2756 0.3137 0.2700 >> 4946 4944 90.00.3164 583.5660 0.3100 >> 606607 90.00.3368 6.6314 0.3300 >> 4949 4946 90.00.3164 620.5243 0.3100 >> 580581 91.90.4030 1003.9232 0.2700 >> 4954 4952 90.30.3164 1.6571 0.3100 >> 580582 89.80.2756 960.9988 0.2700 >> 582583 98.60.2756 592.0677 0.2700 >> 463464 90.00.2654 7.6858 0.2600 >> 581582 88.80.1280 193.0707 0.2700 >> 581583 91.30.2254 514.1149 0.2700 >> Wrote pdb files with previous and current coordinates >> Wrote pdb files with previous and current coordinates >> Segmentation fault (core dumped)" >> >> >> Energy minimization and the NVT equilibration ran without any error or >> warning. The mdp file used is as shown below; >> >> title= Martini >> define = -DPOSRES >> integrator = md >> dt = 0.02 >> nsteps = 5 >> nstcomm = 10 >> comm-grps= >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstenergy= 100 >> nstxtcout= 1000 >> xtc_precision= 100 >> xtc-grps = >> energygrps = Protein W >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> rlist= 1.4 >> coulombtype = Shift >> rcoulomb_switch = 0.0 >> rcoulomb = 1.2 >> epsilon_r= 15 >> vdw_type = Shift >> rvdw_switch = 0.9 >> rvdw = 1.2 >> tcoupl = v-rescale >> tc-grps = System >> tau_t= 1.0 >> ref_t= 300 >> Pcoupl = parrinello-rahman >> Pcoupltype = isotropic >> tau_p= 5.0 >> compressibility = 3e-4 >> ref_p= 1.0 >> gen_vel = yes >> > > If you ran NVT previously, regenerating velocities defeats that purpose > and perturbs the system unnecessarily. Further, Parrinello-Rahman is not > very stable for initial equilibration; use Berendsen and then switch to P-R > for data collec
