Re: [gmx-users] g_msd and MSD analysis
On Sat, 2012-06-09 at 15:33 -0700, Mr Bernard Ramos wrote: Hi everyone! I have a 20 ns simulation (2fs timestep but coordinates saved every 0.2 ps) and I was able to calculate the mean-square-displacement of the oxygen atoms of my water solvent. The entire MSD plot looks very linear to me. I need to fit this set of MSD data to obtain the diffusion coefficient. However, I am not sure if I will have to use the entire MSD points or may be just to consider a few picoseconds at the latter part of the simulation time. In papers I have read, they use up to a 100 ps, although no mention were made as to where those set of points came from. Please help. Hi, have you looked at a linear graph or on a log-log representation. With the latter representation, it is much easier to identify the different regimes of diffusion (ballistic, subdiffusive, and linear). This should allow you to chose an appropriate fit range. Moreover if you fit a straight line to the log-log representation you will immediately see, where the MSD curve deviates from the linear behaviour. /Flo This post seems to suggest a nanosecond window for the analysis of the MSD curve http://lists.gromacs.org/pipermail/gmx-users/2012-January/067487.html Although, this other one suggests using the latter 40 ps of his MSD http://lists.gromacs.org/pipermail/gmx-users/2009-November/046990.html Your help is greatly appreciated. Thanks, Bernard -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD Training
On Sun, 2012-06-03 at 10:47 +0200, Erik Marklund wrote: I once took this course in Amsterdam and can highly recommend it: http://molsim.chem.uva.nl/molsim2012/index.html Me too. Almost all of the PhD students, who join the group where I am currently working in, go there and so far everbody gave the same good respond response. /Flo 31 maj 2012 kl. 19.44 skrev edward.de...@gmail.com: Dear all, does anyone know of any MD or gromacs training course in the coming months? All the best g- -- Sent from my Nokia phone -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Results of the GROMACS user survey NVIDIA board winners
On Fri, 2012-06-01 at 18:09 +0200, Erik Lindahl wrote: Hi, First: Let me thank each and every one of you who took the trouble to fill out our user survey. The resulting information is invaluable to us, and Mark Berger of NVIDIA has been a tremendous help in assembling the results and statistics for us. This WILL affect future development, and we are currently preparing some information from it to put online - stay tuned. However, there was also an incentive part to it ;-) It gives me great pleasure to formally announce the two winners of C2075 cards generously donated by NVIDIA through Mark: * Florian Dommert, Institute for Computational Physics, University Stuttgart * Emmanuel Birru, Monash University, Parkville Campus Big congratulations to both winners from the GROMACS NVIDIA teams, and let me convey a *very* big and special thank-you to Mark Berger for making this possible! Thank you very much for this generous gift. If I consider the tiny amount of time required to complete the survey compared to the effort you spent in the development of GROMACS it was the least I could do. /Flo All the best, Erik -- Erik Lindahl e...@kth.se Professor of Theoretical Computational Biophysics, Royal Institute of Technology Professor of Computational Structural Biology, Stockholm University Tel: +46855378029 (KTH) +468164675 (SU) -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions
Hi, I do not know, how TIP4P/2005 has been parametrized, but the VdW cutoff you are using is quite large. Did the authors of TIP4P/2005 really applied this large cutoff ? This is very important, because the force field is always parameterised in respect to certain parameters and vdW is an essential one. Increasing or decreasing the value suggested by the authors can yield serious artefacts. /Flo On Wed, 2012-05-30 at 15:33 +0800, MD wrote: Hi All, I have to use the long range correction for VDW, in fact i used cut-off=1.4 nm for calculation of surface tension of TIP4P/2005, we can get 65 dyn. The .mdp i used are as follow, I really need to know how to get a surface tension of 69.5 dyn for TIP4P/2005 water model. Becasue my surpervisor is so picky, everything should be perfacet, and i feel really tired by his way. Any comment will be greatly appreciated, The main parameter is coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 The full .mdp are as follow, ; ; File 'mdout.mdp' was generated ; By user: spoel (291) ; On host: chagall ; At date: Mon Dec 15 13:13:06 2003 ; ; VARIOUS PREPROCESSING OPTIONS title = Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 40 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size ; Max number of iterations in relax_shells niter = 20 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 5000 nstvout = 8000 nstfout = 8000 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 5000 nstenergy = 5000 ; Output frequency and precision for xtc file nstxtcout = 500 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.4 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.4 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 3.8 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar)
Re: [gmx-users] dipole moment of a molecule
On Fri, 2012-05-18 at 09:49 -0700, Milinda Samaraweera wrote: Hi Guys Could you please explain to me how to use the g_dipole method to calculate the dipole moment of a Solute in a solvent. Hi, there has just recently been a discussion on this mailing list. Actually you need just an indexfile that contains a group with the solute atoms. Then you just have to choose this group when you execute g_dipoles. However, you have to check the force field, how the partial charges have been parametrised in order to consider the correct electronic polarization. Furthermore, if the solute is charged, there is no unique dipole moment defined, because it will depend on the choice of the origin. In g_dipoles, the COM is chosen as the reference system, if a molecule is charged. /Flo Thanks alot Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Questions about Thermostats
On Tue, 2012-05-15 at 19:47 +0100, Lara Bunte wrote: Hello To make better energy minimization procedures I read about thermostats and barostats. I understand the physical concepts and differences between global and local thermostats and the difference between Berendsen and Nose-Hoover thermostat. 1.) Maybe this question is a little bit hairsplitting, but: This concepts of thermostats and barostats, is this Thermodynamics, is this Kinetics, is this statistical physics? What is it if I want to give this a name. 2.) I read, that local thermostats, i.e. stochastic dynamics produce a NVT ensemble, which is a canonical ensemble and that this alway fulfills Ergodicity Theorem. About this I have following question: In my literature they said, that this means, that all degrees of freedom in the system are coupled strong enough each other. This confuses me. I learned, that ergodicity means, that the complete phase space is passed by a trajectory, if we wait long enough. This means, that ensemble average is equal to time average of the system. Where is in my statement about ergodicity the meaning of all degrees of freedom in the system are coupled strong enough Do this in fact mean, that the complete phase space is passed? 3.) I ask myself what I should use. First question: Local or global thermostat? I guess (not knowing, guessing), that global is better for energy minimization, because as far as I understand, it is more stable than local description. From a physical point of view I think Nose-Hoover shoul be always better, because it produces a real canonical ensemble, while Berendsen is microcanonical ensemble, which is totaly unrealistic?! In an microcanonical ensemble, energy is not changed with the enviroment. This makes no sense? Thanks for helping me Greetings Lara Hi, there has been recently a discussion about this topic on this mailing list. Check the archives for the information you look for. However, Berendsen is not producing any kind of known ensemble, and therefore only applicable for equilibration. /Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Questions about Thermostats
Hi Tsjerk, sorry for the strong statement. I should have said: should be applied ... instead of only applicable. You are right, the question is how big is the difference and actually one would also expect, that the differences vanish with 1/N. However, so far it is unknown, what kind of distributions Berendsen does produce and how this is related to the true canonical ensemble. For this reason, I would be very catious. In my studies I realized big differences in density and dynamical properties, if Berendsen instead of PR is used. Cheers, Flo On Wed, 2012-05-16 at 12:11 +0200, Tsjerk Wassenaar wrote: Hi Florian, Hi, there has been recently a discussion about this topic on this mailing list. Check the archives for the information you look for. However, Berendsen is not producing any kind of known ensemble, and therefore only applicable for equilibration. That's a very strong statement, and scientifically unsound. From a theoretical statistical-mechanical perspective, the ensemble with the Berendsen thermostat does not fall into the known classes. This implies that using the Berendsen thermostat yields a physically different ensemble. Yet the relevant question is whether the ensemble is statistically significantly different, or even practically significantly different. A next question is whether the difference between two simulations with the Berendsen thermostat and two simulations with one of the other ones is consistent or not. And when comparing with experiments, are the predictions with the Berendsen thermostat different from one of the others? This would be a very nice matter of debate if there was a difference in performance using different thermostats. However (unfortunately? ;)) there is not. So for the same cost there are thermostats that do produce the desired ensemble, which makes these preferable over the one from Berendsen (also for equilibration). That is not the same as stating that it is only applicable for equilibration though. For the barostat it's a bit more complicated. Parrinello-Rahman can not be used for equilibration, because a large deviation from the target pressure may well cause large fluctuations that are unphysical and may cause instability. So at the moment the Berendsen barostat appears the only _one_ applicable for equilibration, but that doesn't (yet) disqualify it for further use. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVT conserved-energy lysozyme
On Tue, 2012-05-15 at 09:17 +0100, David de Sancho wrote: Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5. Compiled in double or single precision ? If the latter one is the case, perhaps numerical errors are the reason for the large energy drift. /Flo My concern is with the energy conservation in the implementation of Bussi's velocity-rescaling thermostat. In step 6 of the tutorial an NVT equilibration is run using tcoupl = V-rescale. The temperature equilibrates quite rapidly as shown in Justin's webpage. Essentially, T fluctuates around its equilibrium value after ~ 2 ps. However looking at the conserved energy I find that there is a drift that does not seem to plateau even by the end of the 100 ps run (see attachment). I have tried to sort this out myself by using the following settings: (1) change lincs_iter from 1 to 2. (2) change from PME to PME-Switch, which for NVE Gromacs recommends as more accurate (I also modified: rlist=1.0, rcoulomb=1.0, rvdw=1.4). (3) change to vdwtype = Shift, so that errors due to cutoffs were eliminated. None of this seems to help. Actually Justin himself has helped me and found that with the following settings the conservation is considerably better === shift settings === vdwtype = shift coulombtype = PME rlist = 1.4 rcoulomb = 1.4 rvdw = 1.0 rvdw_switch = 0.8 Still there is a drift in the conserved quantity which seems a quite severe problem. Can anyone give some pointers on how to sort this out? Thanks -David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dipole moment
On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote: Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a point here! g_dipole should do the work XAvier. Hi, I want to point to another problem. If you simulate with a classical force field, you usually have an effective set of partial charges. This means polarization effects are often included in the partial charges. This in turn requires an appropriate calculation of the dipoles. A simple sum over the charges, like g_dipole or g_current does, is not sufficient. The true dipoles are only obtained, if the results from the MD are multiplied with a certain factor the is related to the high-frequency limit of the dielectric constant, the electronic dielectric constant. We have performed several studies on molecular ionic liquids and showed, that with a set of bulk charges, the dipole moments are reproduced correctly, if this electronic dielectric constant is taken into account appropriate. Also for water or any other molecule, the same arguments hold. For example, if TIP4P water is considered. Calculating the dielectric constant gives a value around 50, which is small compared to the exp. value of 80. However, if the correct dipoles are considered, a simulated value of around 80 is the result. Hence, it depends on the parametrization of the partial charges, how the dipole moment or any related property has to be calculated. If you are just interested in the static limit, an effective description with static partial charges is sufficient in my opinion. However, as soon as you are also interested in the time behavior, like the frequency spectrum of the dielectric constant or conductivity, you consider the electronic polarization explicitly with a corresponding force field, as Justin mentioned. Cheers, Flo On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote: Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx-users] dipole moment On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. 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 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] doubts on gen-pairs
On Mon, 2012-05-14 at 11:55 +0200, Bala subramanian wrote: Dear gmx-users, I have some doubts on the manual pages. Kindly help to understand the same. Section 5.7.1 Page 129 1) gen-pairs: Setting ‘yes’ generates 1-4 parameters that are not present in the pair list from normal Lennard-Jones parameters using fudgeLJ. Is there any way that I can see/write the generated parameters in a file. Hi Bala, yes with gmxdump, you can extract all necessary topology information from the tpr file. Section 5.7.1 Page 130 2) Note that gen-pairs, fudgeLJ, fudgeQQ, and N are optional. fudgeLJ is only used when generate pairs is set to ‘yes’, and fudgeQQ is always used. Does it mean that if i specify gen-pairs as no and give the pair parameters explicitly in the topology file, scaling of LJ would be ignored. I simply want to check the consistency in the energies using gen-pair:yes and gen-pair:no (giving the parameters explicitly). 3) Section 5.7.1 Page 130 [ dihedrals ] : …. If you want to include Ryckaert-Bellemans type dihedrals in a topology, do the following (in case of e.g. decane): [ dihedrals ] ; ai aj ak al funct c0 c1 c2 1 2 3 4 3 2 3 4 5 3 and do not forget to erase the 1-4 interaction in [ pairs ]! Someone please help me to understand why the 1-4 interaction should be omitted for RB type dihedrals ?. This is also a point I did not understand, when building the itp files for my ionic liquids. I explicitly checked the influence and realized, that for RB dihedrals the corresponding 1-4 interactions are only calculated, if the respective atoms are listed in the pairs section. No matter how nexcl or gen-pairs is set. Cheers, Flo Thanks, Bala -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dipole moment
On Mon, 2012-05-14 at 12:27 +0200, XAvier Periole wrote: Interesting ... do you have a reference for this? Sure, a detailed discussion about charges for the liquid phase and results for molecular ionic liquids are published in: http://dx.doi.org/10.1039/C1FD00051A and http://pubs.acs.org/doi/abs/10.1021/ct200375v while the theory is based on: http://dx.doi.org/10.1063/1.3060164 and applied to water in: http://pubs.acs.org/doi/abs/10.1021/ct1002048 /Flo XAvier. On May 14, 2012, at 12:01 PM, Dommert Florian wrote: On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote: Hi, You do not need to use the polarizable martini water model to calculate the dipole of molecules. Or I am missing a point here! g_dipole should do the work XAvier. Hi, I want to point to another problem. If you simulate with a classical force field, you usually have an effective set of partial charges. This means polarization effects are often included in the partial charges. This in turn requires an appropriate calculation of the dipoles. A simple sum over the charges, like g_dipole or g_current does, is not sufficient. The true dipoles are only obtained, if the results from the MD are multiplied with a certain factor the is related to the high-frequency limit of the dielectric constant, the electronic dielectric constant. We have performed several studies on molecular ionic liquids and showed, that with a set of bulk charges, the dipole moments are reproduced correctly, if this electronic dielectric constant is taken into account appropriate. Also for water or any other molecule, the same arguments hold. For example, if TIP4P water is considered. Calculating the dielectric constant gives a value around 50, which is small compared to the exp. value of 80. However, if the correct dipoles are considered, a simulated value of around 80 is the result. Hence, it depends on the parametrization of the partial charges, how the dipole moment or any related property has to be calculated. If you are just interested in the static limit, an effective description with static partial charges is sufficient in my opinion. However, as soon as you are also interested in the time behavior, like the frequency spectrum of the dielectric constant or conductivity, you consider the electronic polarization explicitly with a corresponding force field, as Justin mentioned. Cheers, Flo On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote: Dear Justin, Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, May 13, 2012 5:23 PM Subject: Re: [gmx-users] dipole moment On 5/13/12 8:41 AM, dina dusti wrote: Dear GROMACS Specialists, I have one system consists of water and two other molecules. I work by MARTINI CG force field. I want to calculate dipole moment of molecules in water. May I ask you to help me, Please? I doubt you can. Unless you are using version 2.P of the force field (which contains polarizable water), MARTINI uses a single, uncharged particle to represent water. If there are no charges, there is no dipole. -Justin -- Justin A. Lemkul, Ph.D. 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 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org
Re: [gmx-users] rvdw and DispCorr
On Fri, 2012-05-11 at 10:23 +0200, Bernhard Knapp wrote: Dear gromacs users In a recent paper I found the following protocol of a gromacs simulation: All simulations were performed with the GROMACS 4.0 [12] compiled in single-precision mode at a constant temperature of 277 K in a periodic box with an edge length of approximately 8.2 nm and the default GROMOS-96 43A1 forcefield [22]. The simulation systems each contained approximately 16,500 Simple Point Charge (SPC) water molecules [23]. Short-range interactions were evaluated using a neighbor list of 1.0 nm updated at every 10 steps. Van der Waals interactions used a cutoff with a smoothing function such that the interactions slowly decayed to zero between 0.75 nm and 0.90 nm. A long-range analytical dispersion correction was applied to the energy and pressure to account for the truncation of the Lennard-Jones interactions [24]. Electrostatic interactions were evaluated using the particle mesh Ewald (PME) [25] with a real space cutoff of 1.0 nm, a spline order of 6, a Fourier spacing of 0.1 m, and relative tolerance between long and short range energies of . All bonds to hydrogen were constrained with LINCS [26] with an order of 12, and a time step of 2 fs was used for dynamics. In the gromacs manual 4.5.4, page 104 it says: The GROMOS-96 force field was parameterized with a Lennard-Jones cut-off of 1.4 nm, so be sure to use a Lennard-Jones cut-off (rvdw) of at least 1.4. Is it a good idea to set DispCorr to EnerPres and reduce the rvdw so dramatically (almost the half value)? This depends on the sensitivity of force field to these settings. I would try different cut-offs and compare some properties like the mass density. In my studies I often realized that already a small change in the cutoff ~0.1nm may give really different results, though a dispersion correction is applied. This is a results from the procedure, the force field is constructed. Usually all force field parameters are highly correlated. And a second question: Is there a study on the percentage of information getting lost when reducing the rvdw with and without dispcorr (e.g. to 1.2, 1.0, etc) if the forcefield was parameterized with 1.4? So I would expect, that if the system is already homogeneous at rc=0.9 and dispersion correction is applied, a further increase rc should give the same results. However, if the system is not homogeneous at rc, an increase in rc provides more information about the systems. Actually, if there is no very good reason, to chose another cut-off for LJ, as suggested by the force field authors, I would not change it. However, if the homogeneity requirement is met, an small decrease of the cut-off should not introduce too large artefacts. Always keep in mind, that all force field parameters are highly correlated, which includes also the cut-offs, switching or shifting methods, combination rules, ... . The only parameters, where you often have some freedom regard to electrostatics, in case no reaction field method is applied, because then similar considerations as for the LJ cut-off apply. However if an explicit calculation over all charges is used, like in Ewald-based methods, you only have to assure that your settings conform to a certain accuracy, given during the force field parametrization. Cheers, Flo best, Bernhard -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charge derrivation for OPLSAA forcefield
On Tue, 2012-05-08 at 11:38 -0700, Milinda Samaraweera wrote: Hi Guys I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP based charges for some molecules that I study. Is this a correct method to do so if not please let me know what are the other methods that are available. Hi, this is really a hard questions to answer. Different methods to derive partial charges are present, which rely on various ideas. Actually, the partial charges of a force field should be consistent, because they are anyway just an approximation for the true charge density. Common force fields like AMBER or OPLS-AA were constructed with different consideration, giving rise to the differences, though they allow to desribe the same molecules. So I would study, how the remaining parameters of the applied force field were derived. Furthermore be aware that altering a single charge of force field might require readaption of dihedral and LJ parameters. Hence, always be careful and benchmark the force field against single as well collective static and dynamic properties, carefully. /Flo thanks alot Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculation of the components of (ionic) current using g_current
Hi, it is the ionic current, given by a sum over the center of mass velocities of each molecule by their net-charge. /Flo On Mon, 2012-05-07 at 13:00 -0400, Andrew DeYoung wrote: Hi, g_current calculates the (ionic) current in the output file specified by the -o switch (by default, current.xvg). Specifically, each component (x, y, and z) of the current is computed and printed. My question is, is the current that is computed the current of atoms (which each have partial charges), or is it the current of molecules (ionic molecules have non-zero charge, whereas neutral molecules have zero charge)? I am guessing that it is the former -- the current of atoms. However, I am not certain, because when I run g_current, part of the output says, for example: Split group of 6144 atoms into 512 molecules which seems to imply that the code uses the topology (I provide the code with a .tpr file) to determine the connectivity of atoms. Thanks so much! Andrew DeYoung Carnegie Mellon University -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question about ensemble
On Sat, 2012-05-05 at 13:19 +0200, Patrick Fuchs wrote: Interesting discussion indeed. I'm just thinking that there might be no fundamental difference to other thermostats. There's nothing in the way that causes the friction, but then again, there's no physical particle that causes the stochastic term in v-rescale, and the Nosé-Hover particle is not physically touching the atoms either. In all cases the surroundings couples to the atoms in a way that can't be seen in e.g. a test tube. Erik Hi Erik, yes, that is a good point, which I haven't really thought about. Indeed, in a macroscopic system heat will have to diffuse from the edges of the container to the inside of the system. In the simulations, the rescaling of velocities is done on all the atoms at the same time, either on a local or global basis. For the use of SD in explicit systems, the friction and stochastic terms (with the carefully chosen friction coeffictient) can be seen as applying one thermostat per degree of freedom. So Florian, I think you should change your view about the random kicks and friction as a way to modify velocities for thermostating, which is different from mimicking solvant effects in implicit simulations (even if it uses also the friction and random forces). Yes, I know and already did so, as mentioned yesterday. What we want is that the thermostat samples the proper canonical ensemble. Then if it does, what also matters is to be aware whether it affects other properties, notably dynamics (because rescaling velocities will in general pertubs dynamics). There has been a nice discussion some years ago in the GROMACS mailing list about that: http://lists.gromacs.org/pipermail/gmx-users/2008-July/035302.html. Also Bussi and Parrinello discuss this aspect in that paper: http://dx.doi.org/10.1016/j.cpc.2008.01.006. Yes, I am aware of this, too, that is why a careful choice of the parameters is inevitable. Especially, the more you get into detail by reading various literature, the more you realize, that it is really not a simple task to sample an exact canonical ensemble. However, I thank you all again for this discussion, because thermostats and barostats are such an important topic. /Flo Ciao, Patrick -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question about ensemble
On Thu, 2012-05-03 at 18:43 +0200, Patrick Fuchs wrote: Hi Florian, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. The use of Langevin dynamics (SD) to mimic solvant implicitely or as a thermostat in explicit systems depends on the friction coefficient you choose. It has to be chosen with care, see for example http://dx.doi.org/10.1007/b99427 or the GROMACS manual. In explicit simulations, SD with the appropriate choice of friction coefficient can be seen as a local thermostat. The advantage is that it samples the canonical ensemble (in the old versions of GROMACS it was the only way to get the canonical ensemble before the implementation of Nose-Hoover or velocity rescaling). Hi, thank you very much for pointing to this very interesting article. However, though the method seems to work, gamma has a very big influence. I also think, that this kind of coupling is not a good picture for an explicit simulation, because there is nothing in space where friction can arise from, so a reference how to obtain gamma is not given. But thanks everybody of you for the nice discussion. /Flo Ciao, Patrick -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question about ensemble
On Fri, 2012-05-04 at 11:07 +0200, Erik Marklund wrote: 4 maj 2012 kl. 10.45 skrev Dommert Florian: On Thu, 2012-05-03 at 18:43 +0200, Patrick Fuchs wrote: Hi Florian, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. The use of Langevin dynamics (SD) to mimic solvant implicitely or as a thermostat in explicit systems depends on the friction coefficient you choose. It has to be chosen with care, see for example http://dx.doi.org/10.1007/b99427 or the GROMACS manual. In explicit simulations, SD with the appropriate choice of friction coefficient can be seen as a local thermostat. The advantage is that it samples the canonical ensemble (in the old versions of GROMACS it was the only way to get the canonical ensemble before the implementation of Nose-Hoover or velocity rescaling). Hi, thank you very much for pointing to this very interesting article. However, though the method seems to work, gamma has a very big influence. I also think, that this kind of coupling is not a good picture for an explicit simulation, because there is nothing in space where friction can arise from, so a reference how to obtain gamma is not given. But thanks everybody of you for the nice discussion. /Flo Interesting discussion indeed. I'm just thinking that there might be no fundamental difference to other thermostats. There's nothing in the way that causes the friction, but then again, there's no physical particle that causes the stochastic term in v-rescale, and the Nosé-Hover particle is not physically touching the atoms either. In all cases the surroundings couples to the atoms in a way that can't be seen in e.g. a test tube. Erik Hi Erik, yes, that is a good point, which I haven't really thought about. Thanks, /Flo Ciao, Patrick -- ___ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.fu...@univ-paris-diderot.fr Web Site: http://www.dsimb.inserm.fr/~fuchs -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] سلام استاد
Salam, man yekam Farsi fahmam, amma only in Penglish ;) However, perhaps you try English and get more response. Khodafes, Flo On Fri, 2012-05-04 at 04:50 -0700, Hengameh Fallah wrote: Gromacs? نقاشی؟ :) On 5/2/12, leila separdar separdar.le...@gmail.com wrote: salam, man mishnasametun? mozoe naghashie chiye? 2012/5/2 Shima Arasteh shima_arasteh2...@yahoo.com سلام یه خواهش دارم. من بعد قاب کردن نقاشی، ازش عکس نگرفتم. لطفا اگر تونستین برام چندتا عکس خوب بگیرین مرسی میشه لطفا؟ -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question about ensemble
On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question about ensemble
On Thu, 2012-05-03 at 10:45 +0200, Albert wrote: Hello Flo: thank you so much for your kind comments. Yes, I would like to couple the pressure, it really helps a lot. best Albert You're welcome. There is just one little typo On 05/03/2012 10:40 AM, Dommert Florian wrote: On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin it means thermostats and not barostats /Flo provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question about ensemble
On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. /Flo which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo Anyway, I think that there is no strict coupling between temperature and pressure coupling: You need to keep the tempaerature fixed around a value and the same for pressure, so I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is, in priciple, right. Maybe convergence speed changes, but in this case banchmark are quite useful very welcolme! best, Francesco best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- 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
Re: [gmx-users] a question about ensemble
On Thu, 2012-05-03 at 11:31 +0200, francesco oteri wrote: 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. Implicit Implicit solvent means accounting for the solvent presence without including water atoms, look at http://en.wikipedia.org/wiki/Implicit_solvation for details. Regarding the collision source, it is water! The gamma value represent And why do I simulate explicit water, if I have already included water in the collision term ? My question arose because you have written, that Langevin is also applied in explicit water simulations. Now you are only talking about implicit solvent simulations. For this purpose Langevin is surely fine, because it has especially develop for such a situation. /Flo the average collision frequence experienced by a protein atoms against water in solution. You have no water, so it models the water presence. In implicit water simulation, usually a value close to 50 ps-1 (the experimental values) is used, while for explicit water is used a value around 2-5ps-1 bacause water is present so it actually collides with protein. /Flo which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice
Re: [gmx-users] Ion conductivity: current-current (auto)correlation function
On Mon, 2012-04-30 at 13:49 -0400, Andrew DeYoung wrote:
Hi,
Is it possible to compute the ion conductivity using any of the existing
Gromacs tools? Ion conductivity is proportional to the current-current
(auto)correlation function.
For example, the current J_z(t) along z can be written as the sum of the
products of charge and z-component of the speed for each atom in the system:
J_z(t) = \sum_{i=1}^N q_i v_{z,i}(t)
Now, by the Green-Kubo formula, ion conductivity is proportional to the
current-current (auto)correlation function:
\sigma = \frac{1}{3 V k_B T} \int_{0}^{\infty} dt C_{JJ}(t)
where
C_JJ(t) = J_z(0) \cdot J_z(t)
and
... represents an equilibrium ensemble average.
I know that g_velacc computes velocity autocorrelation functions, but is
there any way to compute the current and calculate the current-current
(auto)correlation function?
It seems that g_current calculates the current autocorrelation function, but
do you know what method it uses? Also, is it somehow possible to use
g_current to calculate only the autocorrelation of the current J_z(t) along
z?
Hi,
g_current calculates the ACF for the whole current vector, but it also
gives an output of the current itself. Hence you can choose the z
direction and calculate its ACF with another tool like g_analyze.
However, make sure you save the velocitities frequently enough
(~0.025ps) to obtain a function that is smooth enough for a reasonable
integration.
/Flo
Thank you so very much for your time!
Andrew DeYoung
Carnegie Mellon University
--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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Re: [gmx-users] writing ff parameters as a text file
On Mon, 2012-04-23 at 12:41 -0400, Justin A. Lemkul wrote: On 4/23/12 11:36 AM, Bala subramanian wrote: Friends, I have created the top (attached) file for a tripeptide using pdb2gmx tool of gromacs. However in the top file, i dnt see the pdb2gmx writing the ff parameters. I guess that the ff parameters are read directly from the ff.itp given in the given as #include amber03.ff/forcefield.itp. Is there any way/tool with which i can write these parameters in a separate file. You can view forcefield.itp in a text editor, which will show you that it does little more than point you to other files that hold all of the force field parameters, ffbonded.itp and ffnonbonded.itp. Both of these are also text files that can be viewed very simply. -Justin Hello Bala, if you want all the interactions defined by the force field and put I into the top or itp file. You will have to process the output of gmxdump I think. With the option -sys all bonded and nonbonded parameters are given. Cheers, Flo -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz?
On Fri, 2012-04-20 at 10:33 -0400, Andrew DeYoung wrote: Hi, I am wondering how the fourierspacing parameter corresponds to fourier_nx, fourier_ny, and fourier_nz. The manual (http://manual.gromacs.org/current/online/mdp_opt.html#ewald) says, For ordinary Ewald the spacing times the box dimensions determines the highest magnitude to use in each direction. Will you please help me with an example of this? Suppose I have fourierspacing = 0.24 nm, and my box dimensions are 3.3 nm, 3.3 nm, and 30 nm along x, y, and z. Then what are the values of fourier_nx, fourier_ny, and fourier_nz? fourier_n* is a dimensionless integer, and I don't understand how we can get a dimensionless number from multiplying two quantities that each have dimensions of nm. Should I actually divide the box dimension by fourierspacing, so that (fourier_nx, fourier_ny, and fourier_nz) = (3.3 nm / 0.24 nm, 3.3 nm / 0.24 nm, 30 nm / 0.24 nm) = (13.75, 13.75, 125) ~ (14, 14, 125)? Or am doing this incorrectly? This is the correct calculation. It might be that for scaling issues the final numbers will vary a little bit, but this is not of real importance. Actually you have to assure the error does not get too large. 14 grid points in x and y direction sounds quite few. I would be careful with this settings and hope they are just an example. /Flo Thank you so much for your time! Andrew DeYoung Carnegie Mellon University -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: How does fourierspacing correspond to fourier_nx, fourier_ny, and fourier_nz?
On Fri, 2012-04-20 at 11:35 -0400, Andrew DeYoung wrote: Hi Florian and Mark, Thank you for your time! I am actually using (fourier_nx, fourier_ny, fourier_nz) ~ (14, 14, 125). This is what a colleague who has recommended, although she is using a different (somewhat slower) MD package. One question, if you have time. In that other code, one specifies the maximum number of wave vectors along each (positive or negative) direction. So specifying (14, 14, 125) in that codes means use 14 vectors along +x, use 14 vectors along -x; use 14 vectors along +y, use 14 vectors along -y; use 125 vectors along +z, use 125 vectors along -z. So that corresponds to something like (28, 28, 250) or (29, 29, 251) actual grid points, I think. But in the Gromacs manual (http://manual.gromacs.org/current/online/mdp_opt.html#ewald), I am not sure if fourier_nx, fourier_ny, and fourier_nz specify the number of grid points along x, y, and z or the number of vectors to use along +x and -x; +y and -y; and +z and -z. I think that Gromacs uses the former, but I am not sure. Yes, Gromacs uses the former specification and a setting of 0.12nm Fourier spacing sounds much more reasonable. /Flo Best wishes, Andrew DeYoung Carnegie Mellon University -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: large scale simulation?
On Sat, 2012-03-31 at 15:46 +1100, Mark Abraham wrote: On 31/03/2012 3:40 PM, Albert wrote: Hi guys: thank you very much for your kind comments. Probably the most effective way is to optimize PME balance as Mark mentioned. It seems that Mark's methods improved much much better for the speed. If possible, could Mark share your experience how did you optimize the PME balance in Gromacs? Probably each of us can learn a lot from you. Shameless plug: http://dx.doi.org/10.1021/ct800016r The simulations to which I referred earlier did best with 1:1 PME:PP because of the nature of the hardware. In practice, you can likely do pretty well with Carsten's g_tune_pme in the GROMACS tool set. And a further tool is available, that calculates the error introduced by SPME. It is called g_pme_error and MPI-enabled. In combination with Carsten's tool you can tune your accuracy and speed of calculations. However, be aware that the error estimate only holds for odd interpolation orders. /Flo Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: large scale simulation?
On Sat, 2012-03-31 at 14:23 +0200, Dommert Florian wrote: On Sat, 2012-03-31 at 15:46 +1100, Mark Abraham wrote: On 31/03/2012 3:40 PM, Albert wrote: Hi guys: thank you very much for your kind comments. Probably the most effective way is to optimize PME balance as Mark mentioned. It seems that Mark's methods improved much much better for the speed. If possible, could Mark share your experience how did you optimize the PME balance in Gromacs? Probably each of us can learn a lot from you. Shameless plug: http://dx.doi.org/10.1021/ct800016r The simulations to which I referred earlier did best with 1:1 PME:PP because of the nature of the hardware. In practice, you can likely do pretty well with Carsten's g_tune_pme in the GROMACS tool set. And a further tool is available, that calculates the error introduced by SPME. It is called g_pme_error and MPI-enabled. In combination with Carsten's tool you can tune your accuracy and speed of calculations. However, be aware that the error estimate only holds Sorry that's an error. for odd I meant for even interpolation orders. /Flo interpolation orders. /Flo Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: g_msd with input by trjconv -pbc nojump:a concern
On Tue, 2012-03-20 at 11:38 +0200, Ioannis Beis wrote: Message: 3 Date: Mon, 19 Mar 2012 15:05:43 +0100 From: Dommert Florian domm...@icp.uni-stuttgart.de Subject: Re: [gmx-users] g_msd with input by trjconv -pbc nojump:a concern To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1332165943.4071.82.camel@fermi Content-Type: text/plain; charset=utf-8 Hi and thanks for the reply! Hi, perhaps this problem is related to bug 774: http://redmine.gromacs.org/issues/774 The destination exhibits internal server error, thus I don't have access. which has been discussed quite often, recently. Somehow there is a problem in the order of removing the PBC and jumps. As already mentioned, I could solve the problem by providing a trajectory with whole molecules to g_msd. An indexfile with seperate groups for every molecule has to be created and finally every single molecule group has to be analyzed, but WITHOUT the -mol flag. Afterwards the resulting MSDs only need to be averaged. I used trjconv first with nojump and I used this as input for a subsequent trjconv with mol. Hi, I would not use nojump, because g_msd seems to deal with this correctly, but -pbc whole, perhaps this can solve this problem. /Flo I suppose that's what you mean by providing a trajectory with whole molecules to g_msd. Then I issued g_msd without -mol, providing as index all the atoms of the under interest molecule. The results are still bad. Am I doing something wrong still? Apart from this (which is an additional concern as it seems), my initial question was mostly about whether or not .xtc files carry all information about jumps in addition to coordinates. If the frequency of saving is small, then it might be possible for a molecule to be in two consecutive frames whole, but in the inbetween time it might have jumped. Can trjconv -pbc nojump capture this event? Or is it aware only if it sees the molecule crossing at the very moment of the frame? If the second case is true, then this can have fatal consequencies to MSD calculations. An extreme example: if a molecule moves along 1D in a box that has corresponding vector of length a and between two frames moves by a, then one case gives rise to displacement of a and the other of 0. I would appreciate if someone let me know whether -pbc nojump continuity is unconditional or frequency of saving-dependent. Thank you in advance! Best regards, Ioannis /Flo On Mon, 2012-03-19 at 14:31 +0200, Ioannis Beis wrote: Dear Gromacs users, I have been trying to calculate the lateral MSD of lipid molecules within a bilayer. I have performed simulations in a rectangular box with PBC. I have used trjconv with -pbc nojump. I compared results between the initial trajectory and the one generated by trjconv for 6 different lipids. In 5 cases the calculated MSD was identical and only in one there was difference (big difference). According to the results, MSD loses linearity and exhibits large fluctuations after some point. The above give rise to the following concern. As far as I understand, -pbc nojump checks if any molecule crosses the box boundaries and if yes it brings back the broken part from the symmetric side to the original place, keeping the molecule whole. This way box information is lost, but each molecule is supposed to have continuous trajectories. The true continuity of trajectories, however, is only secured only if .xtc files carry all information of boundary crosses based on the time step of the initial run in addition to all coordinates for all times. Otherwise, the result is clearly dependent on the frequency of saving and continuity is not guaranteed. E.g. in my case -I have small frequency of saving (100 ps) for long simulations to avoid very large output files- one can't tell based merely on the coordinates whether or not a lipid crossed boundaries between two consecutive frames. Of course if the lipid went back and forth then the result of the calculation would not be affected but only by statistical means; however if the lipid had an overall translation across the box (not captured by -pbc nojump because the molecule is whole in both frames), then the calculation is destroyed. If this is the case, it seems to me that g_msd might in practice give correct results for proteins, but for smaller molecules the reliability of the results depends sensitively on molecule size-frequency of saving coordinates relationship and might give rise to huge systematic errors. Is there a way to obtain a converted trajectory that guarantees unconditional continuity, so that one makes sure that he obtains the proper MSD for his molecules? Thank you in advance! Best regards, Ioannis -- Florian Dommert Dipl. - Phys. Institute for Computational Physics
[gmx-users] Ion parameters in OPLS AA force field
Hello, there are several ion non-bonded ion parameters provided in the OPLS-AA files of Gromacs, and the reference from an article Jorgensen et al. from 2001. However I was not able to find the corresponding atom types in this article and so far also not in any other article of the OPLS-AA authors. Does anyone have an idea where these parameters come from ? /Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Ion parameters in OPLS AA force field
On Tue, 2012-03-20 at 14:08 +, Thomas Piggot wrote: Hi Florian, I believe the ion parameters are the Aaqvist parameters: http://pubs.acs.org/doi/abs/10.1021/j100384a009 Cheers Tom Thank you very much for this first important hint. Unfortunately, there parameters of for example La3+, given in GROMACS, are not provided unfortunately. /Flo Dommert Florian wrote: Hello, there are several ion non-bonded ion parameters provided in the OPLS-AA files of Gromacs, and the reference from an article Jorgensen et al. from 2001. However I was not able to find the corresponding atom types in this article and so far also not in any other article of the OPLS-AA authors. Does anyone have an idea where these parameters come from ? /Flo -- Dr Thomas Piggot University of Southampton, UK. -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_msd with input by trjconv -pbc nojump:a concern
Hi, perhaps this problem is related to bug 774: http://redmine.gromacs.org/issues/774 which has been discussed quite often, recently. Somehow there is a problem in the order of removing the PBC and jumps. As already mentioned, I could solve the problem by providing a trajectory with whole molecules to g_msd. An indexfile with seperate groups for every molecule has to be created and finally every single molecule group has to be analyzed, but WITHOUT the -mol flag. Afterwards the resulting MSDs only need to be averaged. /Flo On Mon, 2012-03-19 at 14:31 +0200, Ioannis Beis wrote: Dear Gromacs users, I have been trying to calculate the lateral MSD of lipid molecules within a bilayer. I have performed simulations in a rectangular box with PBC. I have used trjconv with -pbc nojump. I compared results between the initial trajectory and the one generated by trjconv for 6 different lipids. In 5 cases the calculated MSD was identical and only in one there was difference (big difference). According to the results, MSD loses linearity and exhibits large fluctuations after some point. The above give rise to the following concern. As far as I understand, -pbc nojump checks if any molecule crosses the box boundaries and if yes it brings back the broken part from the symmetric side to the original place, keeping the molecule whole. This way box information is lost, but each molecule is supposed to have continuous trajectories. The true continuity of trajectories, however, is only secured only if .xtc files carry all information of boundary crosses based on the time step of the initial run in addition to all coordinates for all times. Otherwise, the result is clearly dependent on the frequency of saving and continuity is not guaranteed. E.g. in my case -I have small frequency of saving (100 ps) for long simulations to avoid very large output files- one can't tell based merely on the coordinates whether or not a lipid crossed boundaries between two consecutive frames. Of course if the lipid went back and forth then the result of the calculation would not be affected but only by statistical means; however if the lipid had an overall translation across the box (not captured by -pbc nojump because the molecule is whole in both frames), then the calculation is destroyed. If this is the case, it seems to me that g_msd might in practice give correct results for proteins, but for smaller molecules the reliability of the results depends sensitively on molecule size-frequency of saving coordinates relationship and might give rise to huge systematic errors. Is there a way to obtain a converted trajectory that guarantees unconditional continuity, so that one makes sure that he obtains the proper MSD for his molecules? Thank you in advance! Best regards, Ioannis -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun - topol.tpr
On Wed, 2012-03-07 at 12:33 +, Lara Bunte wrote: Hi After I used grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr to collect my files into one em.tpr file (which is the meaning of gromp as fas as I understand it) Then I start mdrun for energy minimization with the command mdrun -nt 1 deffnm em You forgot a - in front of deffnm /Flo and got the error Can not open file: topol.tpr What ist the problem? Thank you Greetings Lara -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_msd segmentation fault
On Mon, 2012-03-05 at 23:56 +1100, Mark Abraham wrote: On 5/03/2012 11:39 PM, Gavin Melaugh wrote: Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segmentation fault as follows Select a group: 4 Selected 4: 'SOL' Split group of 16800 atoms into 480 molecules trn version: GMX_trn_file (double precision) Reading frame 800 time 4.000 Segmentation fault However when I perform the same analysis on the solute molecules it runs to completion. I have checked the configuration of the system at frame 800 and everything seems to be fine. I have also analysed the energy and there seems to be no problem. Has anybody any idea of what might be happening? Running out of memory would be the first suggestion. A segmentation fault is a generic error message when a C program (ie. GROMACS) has assumed that it can get access to a certain amount of memory, but is in fact doing so in a way that breaks the rules that segment memory so that one (part of a) program can't hurt another one. Running in single precision will roughly halve your memory requirements, probably without affecting your results. Reducing the number of frames can help also, but it seems you already have fairly few frames. Using -mol probably increases the amount of memory you need by an amount proportional to the number of such molecules (or maybe its square?). Mark However, it seems that the mol flag of g_msd is still buggy as described by: http://redmine.gromacs.org/issues/774 Unfortunately, this bug is still not fixed, though a patch seems to be provided. My workaround for this problem is to convert the trajectory with trjconv using the flag -pbc whole and apply g_msd without the -mol option, but providing appropriate index groups for every single molecule. Unfortunately, this method is very time consuming, because the trajectory has to be read, many many times. Afterwards, I just average the results for the different molecules and derive the diffusion coefficient from the averaged MSD. /Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Positive Coul. recip. term
On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote: The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and the force field is from Lopes (CLaP). I tried deleting all of the cation dihedrals from the itp file and found that the run did not crash, although it still had a positive coul recip term. Upon examination of the cation dihedrals I noticed that there was a typo in which a set of unbonded carbons were put together in a dihedral term. Perhaps this is what made the previous runs crash. Even with this correction, the coul. recip. term is still positive. I have tried smaller time steps and changing ewald_tol to 1e-3, but these have not resolved this issue. How can I calculate the error in the electrostatic force? Denny The error of PME can be estimated a priori with the tool g_pme_error. I would suggest to tune it to a bound below 1e-3. I took a look at the force field parameters for the pyrrolidinium, which is published by Lopes in 2006, and I assume you use this parameters, are you ? I do not understand Table I in this paper. The dihedral parameters are just given for V_2 and V_4, and for a certain dihedral they are even set to zero. If you use this force field, how are the other parameters obtained ? Are they zero or do they correspond to the OPLS values given in the reference cited on the top of the table ? /Flo On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote: Thank you both for your replies. I currently have another ionic liquid running just fine on the same gromacs build (compiled the tpr file yesterday), so I am reluctant to conclude that the problem is with the linking. Please let me know if you disagree. The force field I am using was published in 2004 and has been validated by another group. I have double and triple checked my itp files to make sure they match the force field, but it's possible there are still some errors there. Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who validated it, I am just curious, and what is the ionic liquid ? Though you are constraining the hbonds, I would be cautious with the time step of 2fs, because it might be, that the eigenfrequency of the anionic bonds requires a shorter time step, but this should not be the problem of a positive Coulomb energy. Have you calculated the error in the electrostatic force ? I would suggest to tune it to a limit of 1e-3, perhaps this resolves the problem of the positive Coulomb term. Perhaps some 1--4 and dihedral interactions are missing in the itp file, so assure if all of them are provided correctly. /Flo I agree that this is very strange and feel that there must be something fundamentally wrong in the mdp file or deeper. I have included my mdp file below. title = PMP+TFN cpp = /lib/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 1000 ; total 20 ns nstcomm = 10 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = Cut-off rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = v-rescale tc_grps = PMP TFN tau_t = 0.2 0.2 ref_t = 300 300 nsttcouple = 1 ; Energy monitoring energygrps = PMP TFN ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed
Re: [gmx-users] Positive Coul. recip. term
On Wed, 2012-02-29 at 11:12 -0700, Denny Frost wrote: The parameters I used are from the following reference: Canongia Lopes and Padua, J. Phys. Chem. B 2004, 108, 16893 This paper gives the bonded parameters of the anion and the non-bonded parameters of both ions. The bonded parameters of the cation were obtained (as indicated in the reference above) from the OPLS force field. (Rizzo and Jorgensen, JACS 1999, 121, 4827). Fixing the dihedral error I mentioned in my last email has kept the system from crashing. The coul. recip term is still positive, however. g_pme_error gave a Direct space error estimate of 9.8e-3 kJ/mol*nm and a Reciprocal space error estimate of 3.3 kJ/mol*nm. Look there is a big discrepancy between the real and reciprocal space error, such that your overall force has an error in the order of 10^0, but if you distribute the error over the real and reciprocal part by a change of ewald_rtol, you can descrease this error. g_pme_error with the flag -tune does this for you. Accordingly, by a decrease of the fourier spacing, the error can be further decreased to the desired accuracy. Hence you can check if the positive Coulomb term is an artefact of low accuracy. /Flo On Wed, Feb 29, 2012 at 3:47 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote: The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and the force field is from Lopes (CLaP). I tried deleting all of the cation dihedrals from the itp file and found that the run did not crash, although it still had a positive coul recip term. Upon examination of the cation dihedrals I noticed that there was a typo in which a set of unbonded carbons were put together in a dihedral term. Perhaps this is what made the previous runs crash. Even with this correction, the coul. recip. term is still positive. I have tried smaller time steps and changing ewald_tol to 1e-3, but these have not resolved this issue. How can I calculate the error in the electrostatic force? Denny The error of PME can be estimated a priori with the tool g_pme_error. I would suggest to tune it to a bound below 1e-3. I took a look at the force field parameters for the pyrrolidinium, which is published by Lopes in 2006, and I assume you use this parameters, are you ? I do not understand Table I in this paper. The dihedral parameters are just given for V_2 and V_4, and for a certain dihedral they are even set to zero. If you use this force field, how are the other parameters obtained ? Are they zero or do they correspond to the OPLS values given in the reference cited on the top of the table ? /Flo On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote: Thank you both for your replies. I currently have another ionic liquid running just fine on the same gromacs build (compiled the tpr file yesterday), so I am reluctant to conclude that the problem is with the linking. Please let me know if you disagree. The force field I am using was published in 2004 and has been validated by another group. I have double and triple checked my itp files to make sure they match the force field, but it's possible there are still some errors there. Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who validated it, I am just curious, and what is the ionic liquid ? Though you are constraining the hbonds, I would be cautious with the time step of 2fs, because it might be, that the eigenfrequency of the anionic bonds requires a shorter time step, but this should not be the problem of a positive Coulomb energy. Have you calculated the error in the electrostatic force ? I would suggest to tune it to a limit of 1e-3, perhaps
Re: [gmx-users] Positive Coul. recip. term
On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote: Thank you both for your replies. I currently have another ionic liquid running just fine on the same gromacs build (compiled the tpr file yesterday), so I am reluctant to conclude that the problem is with the linking. Please let me know if you disagree. The force field I am using was published in 2004 and has been validated by another group. I have double and triple checked my itp files to make sure they match the force field, but it's possible there are still some errors there. Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who validated it, I am just curious, and what is the ionic liquid ? Though you are constraining the hbonds, I would be cautious with the time step of 2fs, because it might be, that the eigenfrequency of the anionic bonds requires a shorter time step, but this should not be the problem of a positive Coulomb energy. Have you calculated the error in the electrostatic force ? I would suggest to tune it to a limit of 1e-3, perhaps this resolves the problem of the positive Coulomb term. Perhaps some 1--4 and dihedral interactions are missing in the itp file, so assure if all of them are provided correctly. /Flo I agree that this is very strange and feel that there must be something fundamentally wrong in the mdp file or deeper. I have included my mdp file below. title = PMP+TFN cpp = /lib/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 1000 ; total 20 ns nstcomm = 10 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = Cut-off rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = v-rescale tc_grps = PMP TFN tau_t = 0.2 0.2 ref_t = 300 300 nsttcouple = 1 ; Energy monitoring energygrps = PMP TFN ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= -1 On Fri, Feb 24, 2012 at 12:17 AM, Dommert Florian domm...@icp.uni-stuttgart.de wrote: On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote: Dear all, I am trying to equilibrate a solvent of pure ionic liquid. The system keeps exploding (after 2-5 ns) and I am not sure why, though I believe coulombic interactions are to blame. This is because the Coul-SR term is negative, but the Coul. recip term is very positive throughout the entire run (giving the entire system a positive potential energy). I think this means that the short-range electrostatics are okay, but the long range electrostatics (calculated with PME) are not. Does anybody have any suggestions as to why this would happen? I have used the exact same PME input parameters for another ionic liquid that works just fine. They are listed below. rcoulomb = 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 Depends on the force field you are using. Perhaps it ist not validated for the ionic liquid you want to study. It is especially strange, that it takes so long for your system to blow up. Moreoever I would try to optimize the PME settings with the tools, g_tune_pme and g_pme_error, which give you performance and accuracy of the parameters, respectively. So perhaps with some more information I can provide more help. /Flo Thanks! Denzil Frost -- 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
Re: [gmx-users] Positive Coul. recip. term
On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote: Dear all, I am trying to equilibrate a solvent of pure ionic liquid. The system keeps exploding (after 2-5 ns) and I am not sure why, though I believe coulombic interactions are to blame. This is because the Coul-SR term is negative, but the Coul. recip term is very positive throughout the entire run (giving the entire system a positive potential energy). I think this means that the short-range electrostatics are okay, but the long range electrostatics (calculated with PME) are not. Does anybody have any suggestions as to why this would happen? I have used the exact same PME input parameters for another ionic liquid that works just fine. They are listed below. rcoulomb = 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 Depends on the force field you are using. Perhaps it ist not validated for the ionic liquid you want to study. It is especially strange, that it takes so long for your system to blow up. Moreoever I would try to optimize the PME settings with the tools, g_tune_pme and g_pme_error, which give you performance and accuracy of the parameters, respectively. So perhaps with some more information I can provide more help. /Flo Thanks! Denzil Frost -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problems with martinize.py
On Mon, 2012-02-20 at 16:05 +0100, francesca vitalini wrote: Just one last question Tsjerk, I was trying to load the cg.gro file obtained with martinize in vmd and the program says it is unable to load the molecule. the result of the martinize script looks like: MODEL1 TITLE Protein in water CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 ATOM 1 BB ALA 1 15.063 17.501 13.232 1.00 0.00 ATOM 2 BB GLU 2 14.568 13.732 14.199 1.00 0.00 ATOM 3 SC1 GLU 2 17.373 14.208 15.223 1.00 0.00 TER ENDMDL This looks like a PDB file. If you load cg.gro into VMD it will recognize it as GRO file, but you provide the wrong format. Rename cg.gro to cg.pdb and it should be loaded successfully into VMD. /Flo Does it sound right to you? Thanks 2012/2/20 francesca vitalini francesca.vitalin...@gmail.com: Thank you so much.. Now it is working. I was trying to do it without specifying the secondary structure as I'm having problems with the do_dssp command. It is not working basically and I have to use pdb2gmx to convert into pdb then go to the dssp webpage and create the dssp file from there through the pdb. Do you know a fastest way to make it work? Thanks However, my Martini account never worked, don't know why, so I cannot post it directly. 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hey Francesca, Now there's a small bug in the program. Sorry about it. We'll put the fixed version on in a bit. The problem arises because you don't specify the secondary structure and pymol is not yet available for doing so. The workaround is to explicitly set the secondary structure to loop, by adding -ss LLL on the command line. Thanks for pointing that out. By the way, you might want to post these issues on the Martini forum: http://md.chem.rug.nl/cgmartini/index.php/user-platform/forum It's not exactly Gromacs... Cheers, Tsjerk On Mon, Feb 20, 2012 at 2:34 PM, francesca vitalini francesca.vitalin...@gmail.com wrote: Done while waiting for your e-mail. the error message now says INFO Chain termini will be charged INFO Residues at chain brakes will not be charged INFO Local elastic bonds will be used for extended regions. INFO Position restraints will be generated. WARNINGPosition restraints are only enabled if -DPOSRES is set in the MDP file INFO Read input structure from file. INFO Input structure is a PDB file. INFO Found 1 chains: INFO 1: (Protein), 25 atoms in 3 residues. INFO Total size of the system: 3 residues. Traceback (most recent call last): File ./martinize-1.0.py, line 2415, in module elif options[-pymol]: KeyError: '-pymol' and the pdb looks like TITLE Protein in water REMARKTHIS IS A SIMULATION BOX CRYST1 29.094 29.094 29.094 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 N ALA 1 15.650 18.630 12.470 1.00 0.00 ATOM 2 H1 ALA 1 16.142 19.465 12.716 1.00 0.00 ATOM 3 H2 ALA 1 16.062 18.229 11.652 1.00 0.00 ATOM 4 H3 ALA 1 14.692 18.849 12.287 1.00 0.00 ATOM 5 CA ALA 1 15.730 17.670 13.580 1.00 0.00 ATOM 6 CB ALA 1 15.240 18.220 14.910 1.00 0.00 ATOM 7 C ALA 1 14.970 16.400 13.180 1.00 0.00 ATOM 8 O ALA 1 13.880 16.420 12.610 1.00 0.00 ATOM 9 N GLU 2 15.500 15.310 13.740 1.00 0.00 ATOM 10 H GLU 2 16.295 15.467 14.326 1.00 0.00 ATOM 11 CA GLU 2 15.070 13.910 13.610 1.00 0.00 ATOM 12 CB GLU 2 16.230 12.950 13.880 1.00 0.00 ATOM 13 CG GLU 2 16.930 13.120 15.230 1.00 0.00 ATOM 14 CD GLU 2 17.660 14.430 15.540 1.00 0.00 ATOM 15 OE1 GLU 2 18.650 14.820 14.880 1.00 0.00 ATOM 16 OE2 GLU 2 17.070 15.190 16.330 1.00 0.00 ATOM 17 C GLU 2 13.910 13.480 14.500 1.00 0.00 ATOM 18 O GLU 2 13.760 12.300 14.810 1.00 0.00 ATOM 19 N GLU 3 13.000 14.410 14.790 1.00 0.00 ATOM 20 H GLU 3 13.192 15.329 14.446 1.00 0.00 ATOM 21 CA GLU 3 11.750 14.260 15.550 1.00 0.00 ATOM 22 CB GLU 3 11.920 13.690 16.960 1.00 0.00 ATOM 23 C GLU 3 11.190 15.670 15.730 1.00 0.00 ATOM 24 O1 GLU 3 11.907 16.693 15.192 1.00 0.00 ATOM 25 O2 GLU 3 10.020 15.787 16.413 1.00 0.00 TER can you please explain which the problem is to me? thanks 2012/2/20 Tsjerk Wassenaar tsje...@gmail.com: Hi Francesca, Given the error, it seems there's still a mismatch between the number of atoms and the number indicated. Try
Re: [gmx-users] BD with Hydrodynamic interactions?
On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[Fwd: Re: [gmx-users] BD with Hydrodynamic interactions?]
Forwarded Message From: Sanku M msank...@yahoo.com Reply-to: Sanku M msank...@yahoo.com To: Dommert Florian domm...@icp.uni-stuttgart.de Subject: Re: [gmx-users] BD with Hydrodynamic interactions? Date: Mon, 26 Sep 2011 04:07:38 -0700 (PDT) I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. Please keep correspondence on the mailing list. So how do want to include hydrodynamic interactions into BD ? I think the Lattice-Boltzmann method is a way to do this isn't it ? /Flo From: Dommert Florian domm...@icp.uni-stuttgart.de To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 26, 2011 3:38 AM Subject: Re: [gmx-users] BD with Hydrodynamic interactions? On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: Re: [gmx-users] opls-aa, implicit solvent and GPUs
On Sun, 2011-09-25 at 15:49 +0300, Ehud Schreiber wrote: Hi again, Quoting from the current Gromacs GPUs webpage: Force Fields: Supported FF are Amber, CHARMM. GROMOS and OPLS-AA are not supported. Hello, if read the line above correctly, there is a full-stop after CHARMM. Hence it seems that GROMOS and OPLS-AA are not supported. /Flo Also, it states Forcefields that do not use combination rules for Lennard-Jones interactions are not supported yet. And I don't know whether opls-aa is such a forcefield. So is or isn't it currently possible to accelerate opls-aa on GPUs? Looking at the Roadmap/GROMACS 4.6 webpage, on the up side: Major features (almost) ready to be merged into the 4.6 branch: New GPU non-bonded kernels which work with almost all features of GROMACS. While on the downside: Features currently not supported by the new GPU and SSE kernels: Implicit solvent (but this will still by supported on the GPU through OpenMM) All this led me to my original question. Thanks for your time (and for updating the Roadmap webpage...), Ehud. -- Message: 2 Date: Thu, 22 Sep 2011 10:55:56 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] opls-aa, implicit solvent and GPUs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4e7b4c7c.1010...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed Ehud Schreiber wrote: Hi, I'm currently utilizing gromacs using the opls-aa forcefield in an implicit-solvent setting. Can any of the developers roughly predict in what version, and when, will GPU acceleration be applicable for such work? I am afraid the gromacs 4.6 roadmap webpage left me confused. You can do these simulations on GPU with the current version, or several of the previous releases. -Justin By the way, the main roadmap webpage is totally outdated and needs updating and cleaning... Thanks, Ehud. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ** -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Running two versions of GMX at a time
On Mon, 2011-09-12 at 21:57 +0530, chandran karunakaran wrote: Hi Gmx users, Are we able to run both the lower and higher version at a time? If possible, please help me how to do it. with thanks You can always run different instances of a program at the same time. As you may have recognized the single and double precision versions of GROMACS have a different program suffix by default, such that you can even have both versions in the PATH variable and directory. /Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Force a gromacs tool to write step-by-step a result in a xvg file
Hi, I would suggest you extract the single snapshot from your xtc file and then run the analysis tool on the single snapshot file. /Flo On Tue, 2011-09-06 at 12:12 +0200, intra\sa175950 wrote: Dear All I use the g_clustersize to examine the cluster decay vs. time during the aggregation process of glycolipids into a micelle with the following command: $WORKDIR/gromacs-4.5.3/bin/g_clustsize_mpi -f *.xtc -s run_1.tpr -mc bDM-AMBER99SB-ILDN-Self_b_cluster.xvg -nc bDM-AMBER99SB-ILDN-Self_b_N_cluster.xvg -b 102000 -e 102000 -dt 4 -tu ps -n index.ndx Unfortunately, the program stops with the following error after several steps - Program g_clustsize_mpi, VERSION 4.5.3 Source code file: matio.c, line: 561 Fatal error: Lo: 0.00, Mid: 1.00, Hi: 1.00 - I know that this error comes because I have in my system only one cluster of constant size in my system. Unfortunately, when this error appears g_clustsize_mpi stops and no results for the preceding steps are written in the corresponding xvg files. So it is possible to force g_clustersize (and any others gromacs tools) to write step-by-step a calculation in a *.xvg file. 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] part number in extending simulation
On Sun, 2011-08-28 at 14:21 +0800, Hsin-Lin Chiang wrote:
Hi,
Is part number in extending simulation in ver.4.5.4 cancelled?
Below is my shell script,
#!/bin/bash
a=/stathome/jiangsl/simulation/gromacs/d1GUJ_AB/4md
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.5.4/bin/mdrun \
-nt 12 \
-s ${a}/md100ns.tpr \
-o ${a}/md100ns.trr \
-e ${a}/md100ns.edr \
-g ${a}/md100ns.log \
-c ${a}/md100ns.gro \
-cpo ${a}/md100ns.cpt \
-cpi ${a}/md50ns.cpt
#
In GROMACS ver.4.0.5, if I use this script I'll get files such as
md100ns.part002.trr,
md100ns.part002.gro, md100ns.part002.edr, and md100ns.part002.log.
But in ver.4.5.4 I only get md100ns.trr, md100ns.gro, md100ns.edr, and
md100ns.log.
So, is the function of part number in extending simulation in ver.4.5.4
cancelled?
Hi,
check the standard options of mdrun with the help flag -h of version
4.5.4 and below. You will realize, that the standard append behaviour
changed from no to yes. Hence if you start from a checkpoint and
files are already present in the working directory the integration
results will be appended.
/Flo
Hsin-Lin
--
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Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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Re: [gmx-users] part number in extending simulation
On Sun, 2011-08-28 at 17:55 +0800, Hsin-Lin Chiang wrote: Hi Flo, Thank you for reply. I got it. But as you see I also indicate the new names for output files. Do I get correct result in this kind of situation? Or I need to rerun it with -noappend I am not sure, but I assume if you set new names, new files will be created. The checkpoint input files contains important information about your coordinates, velocities, states of random number generators for the NH coupling That is the reason, why it is necessary for a continuous extension of your run. The results should not depend on the append option, only the number of resulting trajectories is affected. The suffix part??? will just arise if the files are already present and you use -noappend. Now you will end up with two trajectories I assume: * md50ns, * md100ns, which are indistinguishable from a single continuous 100ns run and I think that is what you want, isn't it ? /Flo Sincerely yours, Hsin-Lin Hi, check the standard options of mdrun with the help flag -h of version 4.5.4 and below. You will realize, that the standard append behaviour changed from no to yes. Hence if you start from a checkpoint and files are already present in the working directory the integration results will be appended. Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs: sound wave in liquid?
On Wed, 2011-08-24 at 12:25 -0400, Juliette N. wrote: Dear all, Sorry if my question sounds irrelevant but I am wondering to know if in gromacs there is any tool for studying properties like sound wave/acoustic wave (An acoustic wave is a pressure oscillation that travels through liquid, in a wave pattern)? I dont see such a tool in the manual but I thought maybe someone has an idea how to indirectly extract these information. Please let me know your ideas. Hi, this sounds like a task for a Lattice-Boltzmann code, which is unfortunately not implemented in GROMACS. Moreover as I assume that Coulomb interactions are involved, you perhaps will also get into trouble with momentum conservation, which is hard to achieve with the analytical form of the present SPME. An alternative would be to use the Ewald summation, but this code just runs in serial and for studying sound waves, I assume you need a quite large system, rendering Ewald extremely expensive as it scales with N^(3/2) in the best case. /Flo Thank you all, Regards, J. -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Velocity autocorrelation function
On Thu, 2011-08-18 at 15:44 +0200, Elton Carvalho wrote: On Mon, Aug 15, 2011 at 11:16 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Using g_velacc I can calculate the velocity autocorrelation function of a group as a vector. Can I calculate the velocity autocorrelation function as a scalar? Actually I do not understand what you are pointing at. The velocity autocorrelation function is a scalar property, as it is the dot product of two vectors. Either I apply the -mol flag or not, two lines are contained in vac.xvg: time vs. c(t) However I think the description is outdated. It is claimed that for the mol flag an index group of molecule numbers is required, but if the a group of atoms is provided, it is split into the correct number of molecules. /Flo My naïve suggestion would be to take the norm of that vector. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_dipoles - averaging
On Thu, 2011-08-04 at 15:49 +0100, Kukol, Andreas wrote: Florian, I am not sure, which of the output files of g_current contains the dipole moment for each molecule. Applying g_current to a trajectory of four molecules of asparagin in water gives the following output: To obtain the dipole moment for every single molecule you have to create index groups for every single molecule, and the output you are looking for is the rotational part of M contained in md.xvg the -eps flag is also not necessary and only required for the calculation of the dielectric constant. /Flo g_current -s tpr_200ps.tpr -f xtcIRWhole_100-200ps.xtc -eps 80 -o current.xvg (selecting 4 molecules of asparagin from the index group) md.xvg @title Averaged rotational part of M @xaxis label Time (ps) @yaxis label M\sD\N (enm) @TYPE xy # time x y z average of M_D^2std.dev 0.000 -0.10261 0.12324 0.27085 0.09908 0.31477 0.001 -0.10421 0.12287 0.27297 0.09977 0.31587 0.002 -0.09766 0.12637 0.27104 0.09951 0.31543 ... dsp.xvg @title MSD of the squared translational dipole moment M @xaxis label Time (ps) @yaxis label |M\sJ\N(t)-M\sJ\N(0)|\S2\N / 6.0*V*k\sB\N*T / Sm\S-1\Nps\S-1\N @TYPE xy #Prefactor fit E-H: 1 / 6.0*V*k_B*T: 3.15249e-11 0.000 0 0.001 8.70985e-30 0.002 1.9936e-29 ... mj.xvg @title Averaged translational part of M @xaxis label Time (ps) @yaxis label M\sJ\N (enm) @TYPE xy # time x y z average of M_J^2std.dev 0.000 0.1 0.0 0.0 0.0 0.1 0.001 0.1 0.0 0.0 0.0 0.1 ... current.xvg was not produced due to: ... ... Average volume V=32.764893 nm^3 at T=300.00 K and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 Too less points for a fit.verage volume V=32.764893 nm^3 at T=300.00 K and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 Too less points for a fit. I am not sure, where to find the dipole moment for each of the four molecules. Many thanks Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Dommert Florian Sent: 04 August 2011 12:31 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dipoles - averaging On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote: Hello, Is there any way to output the dipole moment averaged over all molecules or for each molecule separately (and not the total dipole moment of the simulation box) ? Yes, the tool g_current decomposes the total dipole moment into a component in respect to the center of mass of the molecules and a translational term, which is present, if you are dealing with charged species. So, if you prepare a corresponding index file you can derive the average molecular dipole moment for every molecule and finally average the results. /Flo Apparently the dipole autocorrelation function can be obtained as an average over all molecules with the '-corr mol' option, but from the help info it is not clear, how and if the total dipole moment can be obtained in this way (and in which file Mtot.xvg or aver.xvg ?). Many thanks Andreas -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_msd bug
Hello, I can also confirm this behaviour. Furthermore if I use an index group, that just contains 1 molecule and compare the results from an analysis with the flag -mol and without, then I obtain different results which should not be the case. /Flo On Thu, 2011-07-07 at 09:28 +0200, Ivan Gladich wrote: Dear all, I found the same problem that Sławomir pointed out 10 days ago about the memory usage in the computation of g_msd. I have 100 ns simulation for 2880 water molecules. The trajectory is savede every 1 ps: this means that I have 10 frame I think that there is a strange memory problem only when the option -mol is used Indeed, if I use g_msd_d -f ../t230.xtc -s ../t230.tpr -n index.ndx -o msdt230.xvg -b 4000 -e 10 -beginfit 5000 -endfit 25000 -trestart 20 -type x the g_msd does not have any problem by the way using the option -mol (as Sławomir did in the last e-mails) g_msd_d -f ../t230.xtc -s ../t230.tpr -n index.ndx -o msdt230.xvg -b 4000 -e 10 -beginfit 5000 -endfit 25000 -trestart 20 -type x -mol g_msd crashes and memory information (see below) points out that this crash is due by the memory overflow. Thanks a lot Ivan Tasks: 478 total, 5 running, 473 sleeping, 0 stopped, 0 zombie Cpu(s): 0.0%us, 0.5%sy, 12.7%ni, 77.7%id, 9.1%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 65459256k total, 65382420k used,76836k free,0k buffers Swap: 32009508k total, 5360348k used, 26649160k free, 6312k cached On 06/27/11 15:40, Tsjerk Wassenaar wrote: Hi Slawomir, That's quite a usage of memory! Can you provide more information? Like the number of frames in the trajectory, the command line you used, and the system you ran on? Cheers, Tsjerk 2011/6/27 Sławomir Stachurastachura.slawo...@gmail.com: Hi GMX Users, I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amount of memory. With time of calculations the memory reserves are gradually devoured to the extent, in my case, of over 600 GB (than my administrator of cluster killed the process). It seems that it does not release memory and it's pilling results up with steps in memory. Have you heard of such case? Best wishes, Slawomir-- 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 -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Flemingovo nám. 2. 166 10 Praha 6 Czech Republic Tel: +420775504164 e-mail: ivan.glad...@uochb.cas.cz web page:http://www.molecular.cz/~gladich/ - -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] viscosity
On Wed, 2011-06-01 at 23:37 +0200, Thomas Koller wrote: Hello, I calculate the viscosity with g_energy using option -vis (Gromacs 4.0.7): g_energy -f file.trr -s file.tpr -vis visc.xvg Why do I get viscosity values only until the half of the simulation time? This results from the method an autocorrelation function is averaged. For an average that is unbiased you need the same number of samples for every time step. You achieve this by shifting the choice of the value for t=0 through the trajectory. The maximal length of the average you can achieve with this is exactly half the simulation time. /Flo Thomas -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit of ekrot and ektrans
On Tue, 2011-05-31 at 15:31 -0400, Swarnendu Tripathi wrote: Hello everybody, I have a question ragarding the unit of translational and rotational energy. I am using the gromacs-4.0.7 version and it gives these units in the ektran.xvg and ekrot.xvg as kJ mol\S-1\N after I used the command g_traj -f traj.trr -s topol.trr -ekt ektrans.xvg -ekr ekrot.xvg. I was expecting the unit of these quantitites in the unit of energy kJ/mol in gromacs. Any suggestions to convert these to right unit? \S-1\N is just a xmgrace command for a superscript. Plot ektrans.xvg and ekrot.xvg with xmgrace and check which unit appears at the axes labels. /Flo Thank you, -Swarnendu -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Plan for energy minimization, NPT equilibration, and NPT dynamics
Hi Andrew, looking at your protocol, perhaps I can help thermo- and barostating. This are very important issues as they decide if your final trajectory samples a canonical phase space that should correspond to the desired ensemble( Tuckerman and Martyna, J. Phys. Chem. B 2000, 104, 159-178, DOI:10.1021/jp992433y is a very good review for this topic ). You are using Nose-Hoover(NH) for both, equilibration and production. However to drive a system into equilibrium you should perhaps switch to the v-rescale thermostat. It is more stable and samples the phase canonically as well as NH. The shorter you make the coupling time, the faster you reach equilibrium, but the stronger you disturb the correlations in the system. For the production run the NC scheme allows to control the time scales were correlations are affected with the coupling parameter tau_t, while for v-rescale tau_t is just a measure how strong the thermostat is coupled to the system. As you want to simulate a canoncial NPT ensemble, the only possibility for pressure coupling is parrinello-rahman or mttk, while the latter one is just an extension of the first one. However to equilibrate the system berendsen should be the method of choice, though it does not sample canonically. The rules for the coupling parameter are similar as in the case of temperature coupling. For mttk and pr, tau_p is a measure for the time scale where correlations are conserved, while for berendsen tau_p measures the strength of the coupling. For the pressure coupling, short coupling times introduce very large fluctuations of the box size, so that it can take also a very long time to reach equilibrium. Hope this helps a little bit. /Flo On Sat, 2011-05-28 at 21:40 -0400, Andrew DeYoung wrote: Hi, In the past few weeks, I have run some simulations of 254 water molecules. Although I got some results, I did not do things in the best way. For example, I threw away my equilibrated ensemble before doing my production run, as was kindly pointed out to me on this mailing list last week. In trying to think more carefully about the input parameters and the commands I use, I have done some more reading, particularly in the very helpful lysozyme tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lyso zyme/index.html) by Justin Lemkul. In planning another simulation, I would like to understand better reasonable parameters to use and the correct commands to use. If you have time, can you please look at the pdf file at http://www.andrew.cmu.edu/user/adeyoung/may28.pdf that I have created? If you have time, I have some questions about it. On page 1, I have typed some possible parameter files (adapted from Justin Lemkul's lysozyme tutorial); on page 2, I have typed a list of commands (also adapted from the lysozyme tutorial) I may use in my run. I plan to do energy minimization, NPT equilibration, and NPT MD (for NPT, I plan to use Berendsen pressure coupling and Nose-Hoover temperature coupling) using Gromacs 4.5.4. If you have time, here are my questions about the pdf file: --- (i) In equilibration, what is a reasonable value of nstlist to use? The Gromacs manual on page 18 says that nstlist is typically 10, but is it true that, in principle, the smaller that nstlist is (that is, the more often the pairlist is updated), the more accurate the simulation is, at greater computational cost? As a rule of thumb, should I use nstlist = 10 or something smaller? I have access to a cluster, so I don't have too many worries about computational cost, to a reasonable extent. (ii) In equilibration, what is a reasonable value of the time constant tau_p to use for Berendsen pressure coupling? The default is 1 ps, although I have seen tutorials where people use tau_p as high as 2 ps or as low as 0.1 ps. The Gromacs manual on page 32 gives a relationship for the change in pressure with respect to time for Berendsen pressure coupling: dP/dt = (P_0 - P)/tau_p where P_0 is the reference pressure (ref_p in Gromacs). So it seems that the smaller the tau_p, the faster the pressure relaxes toward the reference pressure. So, naively, it would be best to use a small tau_p. However, am I correct in thinking that, on the other hand, if I make tau_p too small for a fixed step size dt, significant inaccuracies may result? (iii) In equilibration, is it reasonable to set DispCorr = no? I won't be using my equilibration results for any detailed analysis; I only wish to generate a (hopefully) reasonable ensemble and relax the pressure to the reference pressure. (iv) Similarly, in production, is it reasonable to set DispCorr = no? I suppose that it depends on what one ultimately wants to calculate using the final MD production results. Since I am still at the stage of getting familiar with Gromacs, I will be doing only simple analyses (RDF, MSD, velocity autocorrelation function, and
Re: [gmx-users] g_current and output redirection
Hello Vitaly, the intention to write out informations to the stdout and the stderr was that you have the ability to sort it during the analysis. However as Justin mentionen will write all open pipes into one file. Cheers, Flo On Tue, 2011-05-10 at 13:16 -0400, Vitaly Chaban wrote: Thanks, Justin! Great solution. On Tue, May 10, 2011 at 12:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Vitaly Chaban wrote: I have a pure linux question. When using g_current and trying to redirect its output to the file, e.g. g_current -temp $TEMPER -b $conduct_b -e $conduct_e EOF output 0 EOF only a part of output is written to the file (output) Here is what is actually written to the file: Selected 0: 'System' Average translational dipole moment M_J [enm] after 25001 frames (|M|^2): 5.554790 -5.833042 -0.539783 (68.255722) Average molecular dipole moment M_D [enm] after 25001 frames (|M|^2): -0.414639 -0.356325 0.148187 (2.359227) Thus, the relevant data (sigma, dielectric constant) are missed. My question is how to redirect all the output of g_current to my file. echo 0 | g_current (options) outfile -Justin Thanks! Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fw: Re: Re: ionic liquids
if you haven't changed anything in the ffoplsaa force field files of gromacs I do not think that you have the correct parametrization. You wether have to define the short range parameters on the top file or you change the ffoplsaa files and insert the parameters of Tsuzuki. How how do this can be found in the manual. /Flo On Tue, 2011-05-03 at 11:36 +0530, Prema Awati wrote: -- Original Message -- From: prem...@iiserpune.ac.in To: vvcha...@gmail.com Date: Tue, 3 May 2011 11:30:00 +0530 (GMT+05:30) Subject: Re: Re: ionic liquids Sir, Thanks for your response !! The LJ parameters are defined in forcefield database so it need not require to be mentioned in topology,I followed gromacs manual.But If its working by adding in the topology,then please guide me regarding LJ parameters. I used OPLS forcefield to create raw topology and then edited referring Tsuzukis. Tsuzuki et.al used basically Lopes et.al forcefield which was refined(partial charges,nonbonding parameters ) to reproduce experimental density. I obtained 1.0045 g/cm3 density which is poor to do final production run in order to study diffusive dynamics of ionic liquids, so I am looking to get exact density that of Tsuzuki. Thanks. -- Original Message -- From: Vitaly Chaban vvcha...@gmail.com To: Prema Awati prem...@iiserpune.ac.in Cc: gmx-users@gromacs.org Date: Mon, 2 May 2011 15:00:19 -0400 Subject: Re: ionic liquids Where are your LJ parameters? Are you sure that Tsuzuki uses all standard OPLS parameters? What density do you get in your simulation? -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 On Mon, May 2, 2011 at 1:59 AM, Prema Awati prem...@iiserpune.ac.in wrote: sir, I am grateful regarding your reply. The reported density for [bmim][bf4] system is 1.198 g/cm3.I was wondering whether you asked for the topology that I am using for my calculation or the one that Tsuzuki.et.al.(one I am referring) have used. Well, following is the toopology that I have created for my system. ; File 'bmim.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Fri Apr 15 18:03:14 2011 ; ; This is a include topology file ; ; It was generated using program: ; Generated by x2top ; ; Command line was: ; g_x2top_d -f boxbmim.pdb -o bmim.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Name nrexcl BIM 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_557 1 BIM NA 1 0.24 14.0067 ; qtot 0.24 2 opls_560 1 BIM CW 2 -0.16 12.011 ; qtot 0.74 3 opls_561 1 BIM CW 3 -0.27 12.011 ; qtot 1.24 4 opls_557 1 BIM NA 4 0.32 14.0067 ; qtot 1.48 5 opls_558 1 BIM CR 5 -0.22 12.011 ; qtot 1.26 6 opls_905 1 BIM C1 6 -0.35 12.011 ; qtot 0.91 7 opls_908 1 BIM C1 7 -0.14 12.011 ; qtot 0.77 8 opls_136 1 BIM C2 8 -0.12 12.011 ; qtot 0.65 9 opls_136 1 BIM CS 9 -0.12 12.011 ; qtot 0.53 10 opls_135 1 BIM CT 10 -0.18 12.011 ; qtot 0.35 11 opls_565 1 BIM HA 2 0.23 1.008 ; qtot 0.41 12 opls_564 1 BIM HA 3 0.27 1.008 ; qtot 0.47 13 opls_563 1 BIM HA 5 0.25 1.008 ; qtot 0.53 14 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.59 15 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.65 16 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.71 17 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.77 18 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.83 19 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.89 20 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.95 21 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.01 22 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.07 23 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.13 24 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.19 25 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.25 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 0.1372 178656.8 1 5 1 0.1340 199576.8 1 6 1 0.1466 141000.8 2 3 1 0.1375 217568.0 2 11 1 0.1080 138490.4 3 4 1 0.1372 178656.8 3 12 1 0.1080 138490.4 4 5 1 0.1340 199576.8 4 7 1 0.1466 141000.8 5 13 1 0.1080 138490.4 6 14 1 0.1090 138490.4 6 15 1 0.1090 138490.4 6 16 1 0.1090 138490.4 7 8 1 0.1516 112131.2 7 17 1 0.1090 138490.4 7 18 1 0.1090 138490.4 8 9 1 0.1529 112131.2 8 19 1 0.1090 138490.4 8 20 1 0.1090
Re: [gmx-users] diverging temperature with pressure coupling
Hello, oh this nasty ILs ;) I am currently investigating a similar problem, that deals with PR-coupling and my impression is that Leap-Frog is the problem and not PR. Currently I am running simulations with md-vv and MTTK to verify my ideas. On the other hand I am using two tc_groups for my ILs due their difference in size. Unfortunately you have not written which IL you deal with, but thinking about long chain ILs like [BMIM][Cl], or [BMIM][PF6], the degrees of freedom for the different molecules differ strongly. Here the big question is why does the barostat influence the thermostat. It seems one has to be very very careful, when choosing the coupling parameter for PR. I did a bunch of simulations just varying the coupling parameter and obtained large differences in the dynamics of my system, while static properties like RDF, density of mass, and pressure look quite fine. For example if I calculate the conductivity including correlation effects the values differ from 2 S/m up to 12 S/m. But so far I also have no idea why ??? I am really happy when I finally got my results with vv and if you are interested I can report back to the list or off-list, just let me know. On the other hand I do not know if the force field could be a problem. PR changes the box size according to a Lagrangian equation of motion in contrast to Berendsen, which just does size rescaling. I do not know how sensible this equations of motions are in respect to the motion of the atoms. Perhaps one can try to perform simulation with a higher accuracy for the electrostatic interactions. I realized that the standard PME settings are quite poor for ILs. Perhaps the Berendsen pressure coupling can deal with this, because it forces the box to scale. PR follows its equations of motions and PERHAPS introduces artefacts if the integration of atomic trajectories is too inaccurate. So my PME settings are like this: rcut=1.3 ( here the force field tells you the number ) pme_order=6 fourierspacing=0.05 rtol=1e-8 This are just approximate values, exact numbers can be calculated by g_pme_error for your system. Cheers, Flo On Sun, 2011-04-17 at 03:10 -0400, Roland Schulz wrote: Forwarding this email from my group colleague: Dear Gromacs users, I am trying to simulate a cellulose fiber in an ionic liquid solution in the NPT ensemble. During the simulation, the entire system is coupled to a thermostat. Yet, I observe an inhomogeneous temperature distribution throughout my system (hot-solvent/cold-solute) when I use Parrinello-Rahman pressure coupling but NOT when I employ Berendsen pressure coupling. I have tested velocity-rescaling and the Nose-Hoover scheme to keep the temperature constant and in both cases Parrinello-Rahman pressure coupling seems to cause the solute’s temperature to become significantly lower than the solvent’s (to decompose temperatures, I am using “mdrun -rerun” with a run input that defines tc_grps separately). I was wondering whether there were any known algorithmic reasons for this unphysical temperature gradient when using Parrinello-Rahman pressure coupling. Thank you. Barmak Comment from me: The effect is large. The ionic liquid is 5 degrees higher and the cellulose is 50 degrees lower (after 50ps, after that it stays constant). With Berendsen pressure both parts fluctuate around the same target temperature (as one would expect). Any reason why one doesn't get the correct temperature with rerun? Or is their a better way to get the temperature for different groups(for a simulation with just one tc-group)? Any reason why Parrinello-Rahman pressure coupling would have this effect on the temperature? Roland -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] diverging temperature with pressure coupling
On Mon, 2011-04-18 at 11:42 +0200, David van der Spoel wrote: On 2011-04-18 11.22, Dommert Florian wrote: Hello, oh this nasty ILs ;) I am currently investigating a similar problem, that deals with PR-coupling and my impression is that Leap-Frog is the problem and not PR. Currently I am running simulations with md-vv and MTTK to verify my ideas. On the other hand I am using two tc_groups for my ILs due their difference in size. Unfortunately you have not written which IL you deal with, but thinking about long chain ILs like [BMIM][Cl], or [BMIM][PF6], the degrees of freedom for the different molecules differ strongly. Here the big question is why does the barostat influence the thermostat. It seems one has to be very very careful, when choosing the coupling parameter for PR. I did a bunch of simulations just varying the coupling parameter and obtained large differences in the dynamics of my system, while static properties like RDF, density of mass, and pressure look quite fine. For example if I calculate the conductivity including correlation effects the values differ from 2 S/m up to 12 S/m. But so far I also have no idea why ??? I am really happy when I finally got my results with vv and if you are interested I can report back to the list or off-list, just let me know. On the other hand I do not know if the force field could be a problem. PR changes the box size according to a Lagrangian equation of motion in contrast to Berendsen, which just does size rescaling. I do not know how sensible this equations of motions are in respect to the motion of the atoms. Perhaps one can try to perform simulation with a higher accuracy for the electrostatic interactions. I realized that the standard PME settings are quite poor for ILs. Perhaps the Berendsen pressure coupling can deal with this, because it forces the box to scale. PR follows its equations of motions and PERHAPS introduces artefacts if the integration of atomic trajectories is too inaccurate. So my PME settings are like this: rcut=1.3 ( here the force field tells you the number ) pme_order=6 fourierspacing=0.05 rtol=1e-8 This are just approximate values, exact numbers can be calculated by g_pme_error for your system. Florian, these PME values are scary! Are you running in double precision too, otherwise I guess it will be difficult to get the errors as low as you want them. Hello David, these settings yield an accuracy of 10^-4 kJ/(mol nm), which should be captured by a single precision calculation, if I take into account that I have forces around 100kJ/(mol nm). Am I wrong ? As regards the Temperature diversion (no pun intended), this is a known issue also with Berendsen T,P coupling. The reason for this is lack of interaction between the different subsystems. It is interesting to hear the PR makes it worse though, because of the better ensemble properties. If this also has an effect on dynamic properties all of us are in even more trouble. I recently had problems reproducing dielectric constants. I will now redo my simulation with Berendsen P-coupling instead of PR, even though grompp tells me not to! So I assume the rerun with Berendsen will give you faster dynamics, which I had when using Berendsen. However as you mentioned you get into problems for creating a correct canonical ensemble. Cheers, Flo Cheers, Flo On Sun, 2011-04-17 at 03:10 -0400, Roland Schulz wrote: Forwarding this email from my group colleague: Dear Gromacs users, I am trying to simulate a cellulose fiber in an ionic liquid solution in the NPT ensemble. During the simulation, the entire system is coupled to a thermostat. Yet, I observe an inhomogeneous temperature distribution throughout my system (hot-solvent/cold-solute) when I use Parrinello-Rahman pressure coupling but NOT when I employ Berendsen pressure coupling. I have tested velocity-rescaling and the Nose-Hoover scheme to keep the temperature constant and in both cases Parrinello-Rahman pressure coupling seems to cause the solute’s temperature to become significantly lower than the solvent’s (to decompose temperatures, I am using “mdrun -rerun” with a run input that defines tc_grps separately). I was wondering whether there were any known algorithmic reasons for this unphysical temperature gradient when using Parrinello-Rahman pressure coupling. Thank you. Barmak Comment from me: The effect is large. The ionic liquid is 5 degrees higher and the cellulose is 50 degrees lower (after 50ps, after that it stays constant). With Berendsen pressure both parts fluctuate around the same target temperature (as one would expect). Any reason why one doesn't get the correct temperature with rerun? Or is their a better way to get the temperature for different groups(for a simulation with just one tc-group)? Any reason why Parrinello
Re: [gmx-users] Re: Trajectory visualization
On Fri, 2011-04-15 at 15:15 +1000, Mark Abraham wrote: On 15/04/2011 3:08 PM, bharat gupta wrote: Reduicng no. of frames means breaking the simulation into smaller frames ... will it affect the result ?? You can use trjconv -dt to reduce the number of frames per unit time, not just chopping into segments. Whether it affects your result is something only you can answer, because only you know what you are trying to do. Mark And if you want to play a little bit around, you can also tell VMD if you want read every step of the xtc file. In the frame section of the molecule file browser, there is an option stride. Increase this number and VMD will read just every n-th step and you can avoid using trjconv for many many times. /Flo On Thu, Apr 14, 2011 at 10:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 15/04/2011 2:49 PM, bharat gupta wrote: Hi, I have done a simulation of 10ns but while viewing the trajectory in VMD I am getting some problems. After loading the .gro and .xtc file VMD stops working .. I used trjconv to compress the file but VMD doesnot read frames from tat file... How can I visualize the trajectories?? How do you mean does not read frames from that file? Can you read an .xtc of one frame? Maybe VMD is running out of memory. Use trjconv to reduce the number of frames and try again. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Unexpected results arising from T- and P-coupling methods
Hello, I have also realized similar behaviour: NpT simulations performed with a Berendsen barostat give lower densities than simulations coupled with P-R. However I think this is due to the fact that I never achieve a pressure of 1bar (it is always around 1.2bar) with P-R even after a previous equilibration of 40ns. I am aware that pressure is a strongly fluctuating quantity and this topic has been discussed for several times on the list, but the equations of motion for the box size given by the Lagrangian for P-R should finally give an average pressure of 1bar even if the fluctuations are large. So what I assume is, that the Leap-Frog integrator is not suitable for this coupling scheme, BUT THIS IS JUST AN ASSUMPTION I DO NOT KNOW, and unfortunately I had no time to try and validate this, yet. /Flo On Tue, 2011-04-12 at 09:13 -0400, chris.ne...@utoronto.ca wrote: I can't tell you if there is a problem or not. The only intended difference that I can see is that for 4.5.X: # grompp by default sets the new nsttcouple parameter equal to nstlist, this means T-coupling is done less frequently; grompp checks if tau_t is large enough # grompp by default sets the new nstpcouple parameter equal to nstlist, this means P-coupling is done less frequently; grompp checks if tau_p is large enough (see http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x ) Note that there were some fixes to P-R scaling in the 4.0.X series -- se http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0 To test this further, I suggest that you need to define a good procedure to ensure that what you are seeing is (b) from a well equilibrated system and is also (b) statistically significant. I suggest that one way to do this is to cycle through your T- and P- coupling options at a given temperature. For example, at T=500 K, run X ns of Berendsen, then X ns of Parrinello-Rahman, then back to Berendsen, and so on for a few cycles. Each time you switch coupling method, be sure to use the structure output from the previous run. Also be sure that X ns is as long as you can afford. This way, you will be able to pick out systematic changes as temperature/density oscillations with periods that are related to your changes of algorithm. This also ensures that what you are seeing is not simply an artifact of having a poorly equilibrated density in your initial structure. You could also run the same cycle with Berendsen and V-rescale. Chris. -- original message -- Dear gmxers, According to my recent practice, we find that the Berensen methods for T- and P- coupling can yield reasonable averaged density as a function of temperature, but when the v-rescale method and the Parrinello-Rahman method are employed for T- and P- coupling, somewhat unexpected results (i.e. density at higher temperature is bigger than that at lower tempearature) are obtained. Generally, the latter setup is considered to be prefered to the former one in simulating realistic ensemble. I am using gmx-4.5.3, and previously I have also performed one similar work using 4.0 which can generate expected results using the latter setup. I wonder if this version 4.5.3 has some bugs in calculating T and P, and are they dealt with in 4.5.4? Please give me some hints. Yours sincerely, Chaofu Wu, Dr. -- Department of Chemistry and Materials Science, Hunan University of Humanities, Science and Technology, Loudi 417000, the People?s Republic of China (P.R. China) -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110412/ceadf085/attachment.html -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dipole moment of a charged peptide
On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: Hi, I have a long-chain peptide which has a net charge of +5 . I was wondering whether the g_dipole will give any reasonable dipole moment for a molecule with a net charge. Is there any suggestion I should follow regarding calculation of dipole-moment of a charged molecule . I found that in the manual it is mentioned that 'For molecules with a net charge, the net charge is subtracted atcenter of mass of the molecule.'. I did not understand what it means. I am using gromacs-4.0.7. Sanku If you have a charged molecule the dipole moment is not unique, so you have to choose a reference point and this can be done by subtracting the net charge at this point. Write down the formula and rearange the terms and you will clearly see, what I mean. Cheers, Flo -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] dipole moment of a charged peptide
On Fri, 2011-04-01 at 09:48 +0200, Erik Marklund wrote: Dommert Florian skrev 2011-04-01 09.45: On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: Hi, I have a long-chain peptide which has a net charge of +5 . I was wondering whether the g_dipole will give any reasonable dipole moment for a molecule with a net charge. Is there any suggestion I should follow regarding calculation of dipole-moment of a charged molecule . I found that in the manual it is mentioned that 'For molecules with a net charge, the net charge is subtracted atcenter of mass of the molecule.'. I did not understand what it means. I am using gromacs-4.0.7. Sanku If you have a charged molecule the dipole moment is not unique, so you have to choose a reference point and this can be done by subtracting the net charge at this point. Write down the formula and rearange the terms and you will clearly see, what I mean. Cheers, Flo And, if I recall correctly, there are two natural choices for this reference pont. One is the center of charge, the other is the center of mass. The latter is perhaps less intuitive, but better related to experimental observables. If you choose the center of charge as reference point, then your molecular dipole moment will be zero, because the dipole moment for a charged molecule can be rewritten as: mu=qtot(x_coq-x_ref) /Flo Erik -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dipole: dipole moment autocorrelation function
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dipole: dipole moment autocorrelation function
On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. In the ionic liquids commmunity dielectric spectra of ILs are usually calulated from equilibrium MD without application of an E-field. The generalized dielectric constant is calculated and a Fourier Laplace transformation finally allows to determine the full dielectric spectrum. Schröder et. al from the University of Vienna have published some articles about this topic. Cheers, Flo Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dipole: dipole moment autocorrelation function
On Thu, 2011-03-31 at 08:53 -0400, Nilesh Dhumal wrote: Thanks Flo for detail reply. Is it possible to put PBC off during calculation of dipole moment autocorrelation function. No, thats the problem, because the volume of the system will increase and dipole density will decrease, this not what you want. However I've written the tool g_current, that allows to calculate the dielectric constant and terms of which it is composed. Read our paper (DOI: 10.1063/1.3030948), which describes the procedure and look at the help, what the programm can do. Cheers, Flo I will run the simulation for 50ns ans try to save trajectroy of 0.02ps. Thanks NIlesh Nilesh On Thu, March 31, 2011 5:38 am, Dommert Florian wrote: On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote: On 2011-03-31 09.25, Dommert Florian wrote: On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote: On 2011-03-30 20.16, Nilesh Dhumal wrote: Thanks. How can I take average. summing up and dividing by the number of sims. How much long I should run the simulation. until the average converges. Nilesh On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote: On 2011-03-30 18.54, Nilesh Dhumal wrote: Hello, I am trying to calculate the dipole moment autocorrelation function for my system (ionic liquid). I am using gromacs 4.0.7 version. Hello, I think you will get into some trouble when you try to calculate an autocorrelation function of property that is not continuous in time. In an ionic liquid you have contributions of the molecular dipole and contribution of the charged molecules to the dipole. The latter part is unfortunately not continuous due to jumping of the molecules over the PBCs. It depends what kind of property you want to calculate, but we experienced that simulations in the range of 50-100ns are required to reliably determine properties like the dielectric constant. The next point is that you have to save your coordinates and velocities quite often ( every 0.02ps we used) Check corresponding literature for further advice. Thanks Florian, for pointing that out. I forgot about it in my previous mail. In order to compute the dielectric constant one could in principle apply constant electric fields at different strengths and then extrapolate to zero. Don't know whether that has been done. In the ionic liquids commmunity dielectric spectra of ILs are usually calulated from equilibrium MD without application of an E-field. The generalized dielectric constant is calculated and a Fourier Laplace transformation finally allows to determine the full dielectric spectrum. Schröder et. al from the University of Vienna have published some articles about this topic. Cheers, Flo Cheers, Flo I run the simulation for 4 ns. I run the following command to calculate the dipole moment autocorrelation function g_dipoles -f water.trr -s water.tpr -corr total -c The function is not geting converge to zero. I want to use this data for calculation of power spectra by fourier transfom of dipole moment autocorrelation function. Can you tell why its not geting converge to zero? You have to simulate at least a few 10s of ns for such slow liquids to converge. Alternatively you can average over many independent simulations (10s). Thanks Nilesh -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
[gmx-users] g_tcaf reference
Hello, g_tcaf gives a reference for the method to calculate \eta. However I can not find the Palmer JCP 49 (1994), either in a database nor on the JCP page. As I want to use the method, I first have to get an idea about it and so I need this article to continue. Has anybody an idea where it is and how to get it ? Cheers, Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_tcaf reference
On Thu, 2011-03-24 at 12:56 +0100, Tsjerk Wassenaar wrote: Hi Florian, It should be Phys. Rev. E i.s.o. JCP. Cheers, Tsjerk Thank you very much, I got it. Cheers, Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
On Thu, 2011-03-17 at 10:44 +0100, Thomas Koller wrote: Hi Nuno, I have still problems with the insatllation of the 4.0.7 version. After unpacking of fftw and gromacs, I did: In the fftw folder: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install export CPPFLAGS=-I$HOME/local/fftw3/include export LDFLAGS=-L$HOME/local/fftw3/lib In the gromacs-4.0.7 folder: ./configure --prefix=$HOME/local/gromacs --enable-shared At the end I get: checking for void*... yes checking size of void*... configure: error: cannot compute sizeof (void*) What does that mean? Why is this not working? This means that the compiler does not work properly. I also encountered this error some time ago, but I can not remember, what the reason exactly was. However I would always go for the latest release and preferably fetch the release branch (check the website for a How To) Cheers, Flo Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: installation of gromacs (Dommert Florian)
On Tue, 2011-03-15 at 05:53 +0100, Thomas Koller wrote: I have installed Gromacs but if I want to open another terminal and run another simulation it does not work. You have to make sure, that the binaries and libraries installed in $GROMACS/bin and $GROMACS/lib are found by the terminal, which can be achieved by sourcing the corresponding GMXRC file. Actually it should work like source $GROMACS/bin/GMXRC However I experienced a hanging terminal for this procedure, but if you choose the script corresponding to your type of console (on Ubuntu you will usually use bash), it should work. So just put the line . $GROMACS/bin/GMXRC.bash or source $GROMACS/bin/GMXRC.bash in your .bashrc (do not forget the . at the beginning of the line), open a new terminal and type: which mdrun This should give you: $GROMACS/bin/mdrun If it does, everything is fine and you can have fun with Gromacs, otherwise post your output, that you can get help. /Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installation of gromacs
Hello, it seems FFTW3 is not installed in the LD_LIBRARY_PATH and/or the fftw3 headers can not be found. On Ubuntu, most likely the headers are not installed (available in the package libfftw3-dev). However it is really easy to compile FFTW3 yourself and install it inside your $HOME. Then you do not get in conflict with your system libraries and no administrator privileges are necessary. Furthermore you can compile FFTW3 with the desired flags for example: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float make -j make install which will install shared fftw3 libs and headers in $HOME/local/fftw3. The flag -sse enables assembler optimization and --enable-float finally gives a single precision library libfftw3f.so . It is strongly suggested to enable assembler to optimize the performance of the FFTW3. Now for the configuration and installation of GROMACS in single precision you can use CMake and or the autotools. For the usage of autotools, the same scheme as describe above applies, however as FFTW3 is not in a standard location, the configure script must be told where to find the required files: CPPFLAGS=-I$HOME/local/fftw3/include LDFLAGS=-L $HOME/local/fftw3/lib ./configure --prefix=$HOME/local/gromacs --enable-shared make -j make install This should install a single-precision version of gromacs with shared libraries in $HOME/local/gromacs. For further specifications ./configure --helps gives many options to choose for example --enable-mpi For CMake the input scheme varies a little bit, but the procedure is the same mkdir build cd build cmake -DFFTW3F_INCLUDE_DIR=$HOME/local/fftw3/include -DFFTW3F_LIBRARIES= $HOME/local/fftw3/lib -DCMAKE_INSTALL_PREFIX=$HOME/local/gromacs make -j make install For CMake a shared build is enabled by default. /Flo On Mon, 2011-03-14 at 13:15 +0100, Diego Enry wrote: The most basic question is: did you install FFTW as root or superuser ? sudo make install If so, try to provide fftw /lib and /include locations (using CPPFLAGS and LDFLAGS) while configuring GMX. (from the Installation Instructions) setenv CPPFLAGS -I/home/joe/fftw/include setenv LDFLAGS -L/home/joe/fftw/lib If your shell is bash: export CPPFLAGS=-I/home/joe/fftw/include export LDFLAGS=-L/home/joe/fftw/lib *If that does not work. Follow cmake instructions. http://www.gromacs.org/Developer_Zone/Cmake ** I have this problem with ubuntu 10.04, even though FFTW is ok I can only Cmake finds fftw. (even providing CPPFLAGS and LDFLAGS) On Mon, Mar 14, 2011 at 1:05 PM, Thomas Koller koller-tho...@gmx.de wrote: Hello, I want to install Gromacs 4.5.3 in my computer. Therefore I downloaded fftw 3.2.2 and did as in the instructions: ./configure --enable-float make make install After that I ran: ./configure with Gromacs, but I always get: checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). Other alternatives are 'fftw2', or 'mkl' for Intel MKL. You are STRONGLY recommended to use one of these - fftw is free. make is not working after this: make: *** No targets specified and no makefile found. Stop. What is going wrong? Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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 -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
