Re: [gmx-users] Gromacs 4.6 4.5.3 qualitative differences 4.6 instability in polarizable force field vacuum/liquid mixture interface simulations
On 2013-11-02 18:38, ploetz wrote: Dear Gromacs Users, Please start a redmine.gromacs.org issue and assign it to me, but try to simplify the system as much as possible. You can cut and paste all the information to the redmine issue. I am trying to simulate a system consisting of a vacuum/condensed phase interface in which a 6x6x12nm condensed phase region is flanked on both ends (in the z-dimension) by a 6x6x12nm vacuum region to form overall box dimensions of 6x6x36 nm. The system is a binary liquid mixture of methanol (0.125 mole fraction methanol) in water using a polarizable (charge on a spring) force field (COS/M methanol and COS/G2 water) at 300K and 1bar. The system is stable in Gromacs 4.5.3; however, mdrun gives a segmentation fault in Gromacs 4.6 when attempting to do dynamics (energy minimization completes with no apparent problems). If I remove the vacuum region, mdrun works. If I incrementally add 2 Angstroms to the z-dimension until I reached a vacuum region of 34 Angstroms total (17 Angstroms on both sides of the condensed phase region) and try to simulate these systems, mdrun works every time. When I reach 36 Angstroms, the segmentation fault re-appears. Although not the system I am actually interested in, I did some simulations using Gromacs 4.6 with the 34 Angstrom vacuum region system and observed an undulating and very turbulant vacuum/condensed phase interface in which a column of water/methanol mixture came out of the condensed phase region to connect the two interfaces. Also, the center of mass motion of the system appeared to not have been removed. In contrast, using Gromacs 4.5.3, the interface is not undulating, but is calm and qualitatively planar, no column forms to connect the interfaces, and there is no problem with the center of mass motion removal. Some of the molecules do enter the vacuum region when running with 4.5.3, but this appears to be due to the movement of individual molecules, not a collective motion of many molecules. This system runs fine with a non-polarizable force field in Gromacs 4.6. I have also compared several properties (using g_energy) of the bulk system (no vacuum region) using Gromacs 4.6 and 4.5.3 and they are not the same for the polarizable force field, but they are the same for the non-polarizable force field. Specifically, with the polarizable force field, the LJ(SR) energy is more positive with 4.6, the LJ(LR) energy is more negative with 4.6, the Coulomb(SR) energy is more negative with 4.6, the Could. recip. energy is more negative with 4.6, the polarization energy is more positive with 4.6, the potential energy is more negative in 4.6, the average kinetic energy (and temperature) is the same but the fluctuations are greater in 4.6, the total energy is more negative in 4.6, the pressure looks fine, and the volume looks fine. Where I've noted differences, these are all statistically significant differences. I would like to know if I can just use 4.5.3 and assume the differences between the results of 4.5.3 and 4.6 are due to some problem in 4.6. I am using all the same input files and commands with both versions, only different executables. I ran the regression tests for 4.6 when I installed it, and passed them all. Sincerely, Elizabeth - ADDITIONAL DETAILS: Below is where the problem appears for the interface system when z-dimension of the vacuum region is = 36 Angstroms total. eq4 is my first attempt at dynamics, after three successful energy minimizations (1st: charges screened and no bond constraints, 2nd: charges felt but no bond constraints, 3rd: charges felt and bond constraints on) [ploetz@cluster AddRemainingVacuumBack]$ grompp -f eq4.mdp -c em3.pdb -o eq4.tpr -n index.ndx -p sys.top -nice 0 :-) G R O M A C S (-: Green Red Orange Magenta Azure Cyan Skyblue :-) VERSION 4.6 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version
Re: [gmx-users] how to calculate kinetic constant?
On 2013-10-04 12:30, Albert wrote: Hello: I've submit a simulation in gromacs, and I am just wondering how can we calculate kinetic constant for the ligand bound/ubound process? thanks a lot Albert Check out our recent paper and references therein: http://pubs.acs.org/doi/abs/10.1021/ct400404q -- 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
Re: [gmx-users] Re: g_hydorder
On 2013-10-01 19:51, Nidhi Katyal wrote: Please provide me with necessary guidance. I have already posted this thrice but have not got a single reply Thanks in advance. On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal nidhikatyal1...@gmail.comwrote: Hello everyone, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n index.ndx I am getting following error; No or not correct number (2) of output files :1 Please give exact command line with file names and output cut-and pasted. The program needs indeed two output files of both types. It seems that your command line is ok nevertheless. Please file a redmine issue and assign it to me. It seems from above that correct number should be 2 but user is supplying only 1 and so is the error. But I am giving names of two output files. Also, I am unable to understand what exactly is contained in these two/four output files. I tried to comprehend this by looking at gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean (variables as defined in program) as the final output. Please help me understand the usage of this command in order to fulfill my aim.I have posted this twice but have not got a single reply. Thanks in advance. -- 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
Re: [gmx-users] confusion about implicint solvent
On 2013-09-23 20:23, Justin Lemkul wrote: On 9/23/13 2:08 PM, Szilárd Páll wrote: Hi, Admittedly, both the documentation on these features and the communication on the known issues with these aspects of GROMACS has been lacking. Here's a brief summary/explanation: - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu which is essentially mdrun + OpenMM, hence it has some limitations, most notably it can only run on a single GPU. The performance, depending on setting, can be up to 10x higher than on the CPU. - GROMACS 4.6: the native GPU acceleration does supports only explicit solvent, mdrun + OpenMM is still available (exactly for implicit solvent runs), but has been moved to the contrib section which means that it is not fully supported. Moreover, OpenMM support - unless somebody volunteers for maintenance of the mdrun-OpenMM interface - will be dropped in the next release. I can't comment much on the implicit solvent code on the CPU side other than the fact that there have been issues which AFAIK limit the parallelization to a rather small number of cores, hence the achievable performance is also limited. I hope others can clarify this aspect. I never got the implicit code to run on more than 2 CPUs, and as I recall Berk hard-coded this due to a limitation involving constraints. It's been a couple years since I tried anything with implicit since (1) the OpenMM support was so buggy and incomplete on GPU and (2) the code ran an order of magnitude slower on CPU than the explicit solvent counterpart. -Justin And finally, even though this is not what you were asking, and likely not wanted to hear either: with implicit solvent your results will not be general enough to be useful, if e.g. hydrogen bonds are important. I would like to recommend my latest paper which shows how solvent entropy and enthalpy contribute in a complex manner to non-bonded interactions in a way that implicit solvent never could: http://pubs.acs.org/doi/abs/10.1021/ct400404q -- 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
Re: [gmx-users] Long range Lennard Jones
On 2013-08-28 09:31, rajat desikan wrote: Hi, What is LJ PME? I googled it and got this publication? http://pubs.acs.org/doi/abs/10.1021/ct400146w So, LJ will not be cut off at some r, but you will have a real+fourier part similar to electrostatics. Is that LJ PME? What are the advantages? http://pubs.acs.org/doi/abs/10.1021/ct400140n On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Lennard-Jones PME is planned for 5.0 Mark On Aug 28, 2013 8:36 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Hi! Just wondering whether gromacs has (or plans to implement) a correction for the loss of long range LJ interactons? Something similar to LJcorrection in NAMD or IPS in CHARMM. Thanks! Gianluca --**--- Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.**washington.edu/ http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. http://healthynaturalbaby.org --**--- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists 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 -- 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
Re: [gmx-users] perl scripts to convert CHARMM ff in GROMACS
On 2013-08-12 21:33, Revthi Sanker wrote: Dear all, The thread on perl,scripts for converting charmm to gromacs states that the package is deprecated and emailed off-list. http://lists.gromacs.org/pipermail/gmx-users/2010-February/048506.html How could I convert charmm to gromacs otherwise? Could anyone help me with their scripts in this regard? http://www.gromacs.org/Downloads/User_contributions/Other_software Thank you for your help in advance. Regards, Revathi -- 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
Re: [gmx-users] hessian calculation with periodic boundary condition
On 2013-08-11 17:00, John Travers wrote: Hi, I am trying to use gromacs to do hessian calculations for some of the structures along a trajectory. Do you know whether the normal mode analysis in gromacs takes into account the periodic boundary condition when computing the 2nd derivative? Thanks! Best JT Yes it does. The parallel version is broken, by the way, a fix is underway. -- 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
Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate
On 2013-08-09 14:29, 朱文鹏 wrote: Hello David, Thank you again for your reply. It is very interesting idea. Do you mean I can using a grand canonical ensemble to control the surface tension of lipid bilayer by varying its number during my simulations? Is there an existing method in Gromacs to implement so? Or I need to modify the Gromacs code? Could you please give me a clue? No this isn't implemented and will be quite hard to do. Why don't you try to make a monolayer of the right size using e.g. http://www.membuilder.org and the place this on the graphene using a text editor. Then if you have the right density and you solvate the layer it will stay a monolayer. In principle you could also put a mixture of lipids and water in the box and it will assemble after a while into a monolayer. I guess you want a monolayer, not a bilayer, and hence you will have to remove one of the two generated layers. And I tried to jump lipids on the 2D periodic graphene layer by adding lipids continuously. Due to the hydrophobicity of lipid tails, the added lipid tails tend to be attached on the graphene layer and form a planar monolayer. But it is not the lipid bilayer I am concerned. If I directly put a periodic lipid bilayer onto the 2D periodic graphene layer, the water molecules between them have no pathway to escape outside. The water permeability through the bilayer is slow in the timescale of MD simulations. The system seems to be time-consuming to find the equilibrium distance between the periodic graphene and the periodic lipid bilayer in MD simulations. Best, Jason --- original message- Message: 2 Date: Thu, 08 Aug 2013 13:41:59 +0200 From: David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate Cc: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 52038407.7000...@xray.bmc.uu.se mailto:52038407.7000...@xray.bmc.uu.se Content-Type: text/plain; charset=GB2312 On 2013-08-08 13:17, 朱文鹏 wrote: Hello David, Thank you for your response. Do you mean a finite lipid bilayer on a periodic infinite graphene layer, or a lipid liposome (or a whole spherical cell) on a periodic infinite graphene layer? A 2D periodic graphene layer - which will be an infinite molecule, and then just dump lipids on them, which will form a periodic monolayer. You control the surface tension of the lipids by varying the number. How you would compute the surface tension then is another problem. For the first case, how do you control the surface tension of lipid bilayer? For the second case, I cannot set up a very large spherical cell due to the computational cost. If it is too small, it will be different from the actual situation. Best, Jason --- original message --- Message: 1 Date: Thu, 08 Aug 2013 08:37:15 +0200 From: David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 52033c9b.4040...@xray.bmc.uu.se mailto:52033c9b.4040...@xray.bmc.uu.se mailto:52033c9b.4040...@xray.bmc.uu.se mailto:52033c9b.4040...@xray.bmc.uu.se Content-Type: text/plain; charset=UTF-8; format=flowed On 2013-08-07 22:50, 朱文鹏 wrote: Dear all, I am trying to set up an all-atom MD simulation to investigate the interaction between lipid bilayer and infinite substrate of graphene or graphene oxide. The edge effects of graphene and graphene oxide are not what I am concerned. The lipid bilayer is placed on the substrate parallelly in the x-y direction. I know the pressure coupling method of surface-tension can control the surface tension in the x-y plane. But it is only for the whole system. The lipid layer and graphene substrate are both infinite in the x-y direction. Can I control the pressure of lipid bilayer and infinite substrate separately? Otherwise, should I change the lipid bilayer to a finite one but still with zero surface tension, or change the graphene substrate to a finite one but without edge effects? How can I remove the edge effects from a finite graphene or GO layer? Do you have any suggestions? I will very appreciate that. Looking forwards to your reply. Why not make a periodic graphene layer (you will have to generate the topology yourself)? You can put anything you like on top of it, and the have pressure coupling only in the normal direction. Best, Jason -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205 tel:%2B46184714205 tel:%2B46184714205. sp
Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate
On 2013-08-07 22:50, 朱文鹏 wrote: Dear all, I am trying to set up an all-atom MD simulation to investigate the interaction between lipid bilayer and infinite substrate of graphene or graphene oxide. The edge effects of graphene and graphene oxide are not what I am concerned. The lipid bilayer is placed on the substrate parallelly in the x-y direction. I know the pressure coupling method of surface-tension can control the surface tension in the x-y plane. But it is only for the whole system. The lipid layer and graphene substrate are both infinite in the x-y direction. Can I control the pressure of lipid bilayer and infinite substrate separately? Otherwise, should I change the lipid bilayer to a finite one but still with zero surface tension, or change the graphene substrate to a finite one but without edge effects? How can I remove the edge effects from a finite graphene or GO layer? Do you have any suggestions? I will very appreciate that. Looking forwards to your reply. Why not make a periodic graphene layer (you will have to generate the topology yourself)? You can put anything you like on top of it, and the have pressure coupling only in the normal direction. Best, Jason -- 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
Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k
On 2013-08-08 01:16, Golshan Hejazi wrote: Hello, I have performed quit a lot of tests and I have some question: I have an amber.crd and amber.top files ... I perform a single step energy calculation with amber , gromacs and cp2k. in all of them I am using amber force field but the point is that in cp2k and amber, I am reading crd and top file directly while in gromacs, i need to convert them to gromacs format. I performed this test for a simple ace-ala-nme system. Lets talk only about the BOND, ANGLE and TORSION energies which are the same in all of these packages. these energy components output are identical in amber and cp2k. However, there is a big difference between them and gromacs: cp2k, amber ... BOND= 0.0206 (kcal/mol) ANGLE=0.3620 (kcal/mol) TORSION=8.1071 (kcal/mol) gromacsBOND=0.14044 (kcal/mol) ANGLE=0.3780 (kcal/mol) TORSION=9.74190 (kcal/mol) The other terms are also different. But lets focus on these because they are the same in all these packages. Now, how did i convert the crd and top file to gromacs fromat? 1- I tried amb2gmx perl script 2- I used ambpdb of amber to generate a pdb file and then pdb2gmx of gromacs to generate the top and gro file for gromacs BOTH of these ways gives different results from each other and also from cp2k and amber! I would really appreciate any help about this problem ... it seems to me there is a bug in amber to gmx file convertors?! it looks like some kind of rounding error, pdb file have limited precision. the force constants you can check yourself. Thanks Golshan -- 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
Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate
On 2013-08-08 13:17, 朱文鹏 wrote: Hello David, Thank you for your response. Do you mean a finite lipid bilayer on a periodic infinite graphene layer, or a lipid liposome (or a whole spherical cell) on a periodic infinite graphene layer? A 2D periodic graphene layer - which will be an infinite molecule, and then just dump lipids on them, which will form a periodic monolayer. You control the surface tension of the lipids by varying the number. How you would compute the surface tension then is another problem. For the first case, how do you control the surface tension of lipid bilayer? For the second case, I cannot set up a very large spherical cell due to the computational cost. If it is too small, it will be different from the actual situation. Best, Jason --- original message --- Message: 1 Date: Thu, 08 Aug 2013 08:37:15 +0200 From: David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Lipid Bilayer on the Graphene or GO substrate To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 52033c9b.4040...@xray.bmc.uu.se mailto:52033c9b.4040...@xray.bmc.uu.se Content-Type: text/plain; charset=UTF-8; format=flowed On 2013-08-07 22:50, 朱文鹏 wrote: Dear all, I am trying to set up an all-atom MD simulation to investigate the interaction between lipid bilayer and infinite substrate of graphene or graphene oxide. The edge effects of graphene and graphene oxide are not what I am concerned. The lipid bilayer is placed on the substrate parallelly in the x-y direction. I know the pressure coupling method of surface-tension can control the surface tension in the x-y plane. But it is only for the whole system. The lipid layer and graphene substrate are both infinite in the x-y direction. Can I control the pressure of lipid bilayer and infinite substrate separately? Otherwise, should I change the lipid bilayer to a finite one but still with zero surface tension, or change the graphene substrate to a finite one but without edge effects? How can I remove the edge effects from a finite graphene or GO layer? Do you have any suggestions? I will very appreciate that. Looking forwards to your reply. Why not make a periodic graphene layer (you will have to generate the topology yourself)? You can put anything you like on top of it, and the have pressure coupling only in the normal direction. Best, Jason -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205 tel:%2B46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se http://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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding gromos method in g_cluster
On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my MD trajectory using gromos method under g_cluster module. I got one doubt regarding the output, as I used the cutoff of 0.3nm for RMSD calculation, I was expecting that all the snapshots which have RMSD less than or equal to 0.3nm will form the first cluster and the rest of snapshots will form another cluster. But the output gives a single cluster. Please let me know if I have not understood it correctly. It means everything is within 0.3 nm RMSD from each other. Maybe your system is very stable or you did not simulate very long. You can use a shorter cut-off. I am appending the output below: Using gromos method for clustering Using RMSD cutoff 0.3 nm The RMSD ranges from 0.0602553 to 0.411066 nm Average RMSD is 0.107366 Number of structures for matrix 12501 Energy of the matrix is 960.075 nm Found 1 clusters Writing middle structure for each cluster to clusters.pdb Counted 0 transitions in total, max 0 between two specific clusters ## -- 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
Re: [gmx-users] Regarding gromos method in g_cluster
On 2013-07-31 09:45, bipin singh wrote: Thanks for the reply Prof. David. But in the output it shows that The RMSD ranges from 0.0602553 to 0.411066 nm; this is the point of confusion to me. So I think it should write the snapshots having RMSD greater than 0.3nm (cutoff) to another cluster. I see, then maybe the definition is different (check the source code!). It could be that it is 0.3 nm from the cluster center. On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my MD trajectory using gromos method under g_cluster module. I got one doubt regarding the output, as I used the cutoff of 0.3nm for RMSD calculation, I was expecting that all the snapshots which have RMSD less than or equal to 0.3nm will form the first cluster and the rest of snapshots will form another cluster. But the output gives a single cluster. Please let me know if I have not understood it correctly. It means everything is within 0.3 nm RMSD from each other. Maybe your system is very stable or you did not simulate very long. You can use a shorter cut-off. I am appending the output below: ##**## Using gromos method for clustering Using RMSD cutoff 0.3 nm The RMSD ranges from 0.0602553 to 0.411066 nm Average RMSD is 0.107366 Number of structures for matrix 12501 Energy of the matrix is 960.075 nm Found 1 clusters Writing middle structure for each cluster to clusters.pdb Counted 0 transitions in total, max 0 between two specific clusters ##** -- 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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] Limitations of simulations?
On 2013-07-24 01:57, Jonathan Saboury wrote: I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually have it complex with the protein. Obviously, if it could do this it would take a much longer time than just simulating a complex, but if given enough time, could it complex? Yes, there are some examples. A paper was published by Shaw and co-worker in J. Amer. Chem. Soc. a year or two ago. I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! Thank you! :) -- 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
Re: [gmx-users] g_hbond for trajectory without having box information
On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- 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
Re: [gmx-users] Re: g_velacc
On 2013-07-05 10:50, Ishwor wrote: I have taken the fit for 2ns in Einsteins curve to calculate the diffusion coefficient but when i take the values up to 100 ps for velocity auto correlation i get the matching result...Is it good to do such thing? i will be happy if you guide me. I have attached the graph of VAC herewith. Thanks http://gromacs.5086.x6.nabble.com/file/n5009582/vac.jpeg -- View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009582.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. The graph does not show the tradition ripples. If this is for water the result could be ok with 100 ps, but you still need to have decent sampling (e.g. 20 fs) of the velocities since they change rapidly. -- 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
Re: [gmx-users] FW: Inconsistent results between 3.3.3 and 4.6 with various set-up options
values made negligible difference. So in summary: 1) GPUs still look a bit dodgy, particularly at pressure coupling, and 2) There seems to be something fundamentally different between the way things are being calculated between 3.3.3 and 4.6 on CPUs as well. Would this be due to the Trotter scheme that Berk Hess mentioned here: http://gromacs.5086.x6.nabble.com/Reaction-Filed-crash-tp4390619p4390624.html ? Will I have to stick with 3.3.3 for as long as I want to be able to compare to existing results? Thanks in advance, Long story, but thanks for checking. You might want to see what nstcalcenergy = 1 does for your 4.6 results in particular the fluctuations. The difference in kinetic energy could come from a changed notation for continuation runs in the mdp file. Cara Example .mdp file: integrator = md dt = 0.002 ; 2fs nsteps = 225 ; 4.5ns comm_grps= DOPC SOL nstxout = 1000 nstvout = 1000 nstlog = 1000 nstenergy= 1000 energygrps = DOPC SOL cutoff-scheme= group nstlist = 5 ns_type = grid pbc = xyz rlist= 0.8 coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 62 vdwtype = Cut-off rvdw = 1.4 tcoupl = berendsen tc-grps = DOPC SOL tau_t= 0.1 0.1 ref_t= 303 303 Pcoupl = berendsen pcoupltype = semiisotropic tau_p= 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p= 1.0 1.0 gen_vel = no constraints = all-bonds constraint_algorithm = lincs continuation = yes -- 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 -- 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_velacc
On 2013-07-04 08:32, Ishwor wrote: I have really tried to calculate diffusion coefficient using both commands but i cant find the comparable results. i have my *.mdp file as ;PREPROCESSING parameters tinit = 0 integrator = md dt =.002 nsteps = 1 nstcomm = 1 ;OUPUT CONTROL parameters. nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstxtcout = 500 energygrps = system ;NEIGHBOUR SEARCHING parameters. nstlist = 10 ns_type = grid rlist = 1.0 ;ELECTROSTATIC and VdW parameters. rcoulomb= 1.0 rvdw= 1.0 epsilon-r = 1 ;BERENDSEN TEMPERATURE COUPLING is on in two groups Tcoupl = berendsen tc-grps = system tau_t = 0.1 ref_t = 303 ;PRESSURE COUPLING is on Pcoupl = no gen_vel = no; ;BONDS parameters constraints = all-bonds constraint-algorithm = shake unconstrained-start = yes pbc = xyz i have calculated the diffusion coefficient using Einsteins law and found 2.40*10^-5 cm^2/s. I have used 2 ns time to fit the curve. To calculate the diffusion coefficient using g_velacc i used the command g_velacc -f nvt.trr -s nvt.tpr -n index.ndx -o vac.xvg -nonormalize -acflen 2001 -mol and integrate using g_analyze -f vac.xvg -integrate but i found the result Calculating the integral using the trapezium rule Integral 1 0.11915 +/-0.0 std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 1.262569e-04 5.975760e-03 1.336220e-04 27.976 664.233 I guess the required integral value is 0.11915 and to find diffusion coefficient i divide the result by 3 but get the result not matching with the one found using g_msd. i guess the value 0.11915 is in unit nm^2/ps. I dont know whether i am in the correct path or there is some problems with my doings. i am waiting for the suggestions nstvout = 10 Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009543.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] g_velacc
On 2013-07-04 05:38, Ishwor wrote: Dear all I have calculated the diffusion coefficient using command g_msd and I want to calculate diffusion coefficient using command g_velacc. I am confused with some terms. 1I have looked the manual page of g_velacc and i found the statement the time interval between data collection points is much shorter than the time scale of the autocorrelation. What actually does that mean? 2I am also confused with the flag -acflen ( I have found that it describes the number of frames to be taken into consideration.Does that mean I have to take the points ,to integrate, in such a way that it matches with the time i have used in g_msd for fitting of Einsteins equation) 3 what does the flag -nonormalize indicates. Do I need to use it necessarily? 4Is the command g_analyze -f *.xvg -integrate sufficient for integration? Ishwor Lots of good questions. Have you actually tried? You need to store the Velcoties quite often, maybe every 20 fs (depending on the system). Nepal -- View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] How to modify the code g_hbond to analyze the non-traditional hydrogen bonds like C-H...O
On 2013-06-30 11:34, Wu Chaofu wrote: Dear gmxers, I want to analyze the non-traditional hydrogen bonds like C-H...O. To my best knowledge, the g_hbond code can be used for traditional hydrogen bonds but not for our case. One possible solution is to modify the g_hbond code to include the non-traditional hydrogen bonds. However, the code is too long and too complex to understand for me, a non-programmer. Could you give me hints to cope with this, please? Thank you very much for any replies! Yours sincerely, Chaofu Wu g_hbond will be rewritten from scratch more or less for 5.0 therefore I would like to try to discourage modifications. That said, a small hack in search_donors() should do the trick. -- 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
Re: [gmx-users] ***using output of dl_poly in gromacs??***
On 2013-06-25 21:52, hamid mosaddeghi wrote: Dear all I did some bio simulation by dl_poly ,is it possible use gromacs for analysis data? Best Of Luck sure,if you can output the sim as e.g. a pdb file with multiple frames/models. Some analysis tools need a gromacs topology file which is easy to make for proteins/nucleic acids. Run a gromacs tutorial if you haven't yet. -- 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
Re: Fw: [gmx-users] ***using output of dl_poly in gromacs??***
On 2013-06-26 09:14, hamid mosaddeghi wrote: Dear David thansk for quick reply, but existed one problem, my system include metal and protein that metal not define in gromacs then writing topology is difficult, how do analysis with gromacs without write toplogy? any suggestion will be appreciated for some analysis you do not need it at all. For some analysis you could also leave out the metal (e.g. secondary structure of protein). - Forwarded Message - *From:* David van der Spoel sp...@xray.bmc.uu.se *To:* gmx-users@gromacs.org *Sent:* Wednesday, 26 June 2013, 11:10 *Subject:* Re: [gmx-users] ***using output of dl_poly in gromacs??*** On 2013-06-25 21:52, hamid mosaddeghi wrote: Dear all I did some bio simulation by dl_poly ,is it possible use gromacs for analysis data? Best Of Luck sure,if you can output the sim as e.g. a pdb file with multiple frames/models. Some analysis tools need a gromacs topology file which is easy to make for proteins/nucleic acids. Run a gromacs tutorial if you haven't yet. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. mailto: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 -- 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: Enthalpy Confusion
On 2013-06-14 19:28, Jeffery Perkins wrote: or should i be doing U+V*ref_p = H? More specifically, U + V*ref_p = H H isn't really meaningful thing. I mean, you can define something such that H* = H, but that's not really thermodynamics. sorry I always have issues deciding how to talk about this stuff, so thanks for putting up with my terrible notation =) example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either Interesting. What material at what phase conditions? For liquids, the PV contribution should be very small. I hadn't really thought about that... but the system is a monatomic Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass = 40 amu) which should be a liquid at the conditions I was looking at, P=1000 bar, T = 300 K using phase diagram in: Equation of state for the Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37, No. 5, 1429-1454 the U is -1600 and the pV is 880 when manually done, around 400 from g_energy Here's the code: /* This is pV (in kJ/mol). The pressure is the reference pressure, not the instantaneous pressure */ pv = vol*md-ref_p/PRESFAC; add_ebin(md-ebin, md-ipv, 1, pv, bSum); enthalpy = pv + enerd-term[F_ETOT]; What is your volume? What is Etot? a bit messy but this is data from g_energy for the system with increasing temperature (300 K-1000 K), and constant pressure of 1000 bar (so 100 000 000 Pascals): Temperature VolumeEnthalpy Potential Total EnergypV Kinetic En. K nm^3 kJ/molkJ/mol kJ/mol kJ/mol kJ/mol 299.914 14.7226 -1168.83 -2565.44-1611.63442.791 953.817 399.901 17.462 -339.795 -2080.31-808.501468.706 1271.81 499.898 21.0263 421.763 -1666.7 -76.8794498.643 1589.83 599.899 25.1149 1088.79 -1348.14559.718 529.07 1907.86 699.914 29.4219 1668.2-1115.471110.46 557.733 2225.94 799.925 33.7642184.31 -943.6131600.39 583.922 2544 899.923 38.0865 2660.3 -809.5722052.45 607.847 2862.03 999.931 42.2798 3101.56-707.9082472.17 629.383 3180.08 all uncorrected for the number of particles in the box (so Etot is in kJ/256 mol of particles) when i use this data to get H myself i get: H kJ/mol -725.32948 242.7114 1188.90386 2071.63498 2881.65838 3632.9828 4345.2573 5017.41396 again uncorrected for the number of particles in the box Thoughts? Your calculation seems correct. Which gmx version did you use? The correlation between the numbers is almost 100% so there must be a simple explanation. -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009164.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] Re: Enthalpy Confusion
On 2013-06-14 21:39, Jeffery Perkins wrote: Your calculation seems correct. Which gmx version did you use? The correlation between the numbers is almost 100% so there must be a simple explanation. gmx version is 4.5.4, and yeah the correlation is odd, in the code you listed: Then that is the reason. I forgot about it, but the calculation of pv is incorrect in that version. If you use 4.5.7 or 4.6.2 it should be fine. pv = vol*md-ref_p/PRESFAC; add_ebin(md-ebin, md-ipv, 1, pv, bSum); enthalpy = pv + enerd-term[F_ETOT] so pv = vol * md-ref_p/PRESFAC; is the vol * ref_p/conversion factor, right? the only thing there that seems like it could be off is if PRESFAC isn't correct for some reason (correct me if I'm wrong of course!) Jeffery -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009168.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] Re: Enthalpy Confusion
On 2013-06-11 23:31, Jeffery Perkins wrote: or should i be doing U+V*ref_p = H? More specifically, U + V*ref_p = H H isn't really meaningful thing. I mean, you can define something such that H* = H, but that's not really thermodynamics. sorry I always have issues deciding how to talk about this stuff, so thanks for putting up with my terrible notation =) example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either Interesting. What material at what phase conditions? For liquids, the PV contribution should be very small. I hadn't really thought about that... but the system is a monatomic Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass = 40 amu) which should be a liquid at the conditions I was looking at, P=1000 bar, T = 300 K using phase diagram in: Equation of state for the Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37, No. 5, 1429-1454 the U is -1600 and the pV is 880 when manually done, around 400 from g_energy Here's the code: /* This is pV (in kJ/mol). The pressure is the reference pressure, not the instantaneous pressure */ pv = vol*md-ref_p/PRESFAC; add_ebin(md-ebin, md-ipv, 1, pv, bSum); enthalpy = pv + enerd-term[F_ETOT]; What is your volume? What is Etot? PRESFAC ~ 16.6 -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009068.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] Enthalpy Confusion
On 2013-06-11 20:09, Jeffery Perkins wrote: This may just be me not understanding what I'm looking at, but I'm trying to get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4 initially I've tried using the enthalpy option in g_energy but I noticed that if i compare that value to H=U+pV using either the average or the instantaneous values from g_energy switched over to SI so that there is no issue there, the results are different (manual calculation is around 2x the g_energy result). So the question is, what am I overlooking in the analysis of the data i have? The calculation is done inside mdrun and it provides H = Etot + pV where p is the applied pressure (typically 1 bar). Is this the same that you did? -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] Re: Enthalpy Confusion
On 2013-06-11 21:57, Jeffery Perkins wrote: If you are computing enthaply in the NPT ensemble, P is constant, and is the applied pressure. The pressure quantity calculated from the KE and the virial is not the pressure. It is a quantity that when averaged over time is equal the pressure. Only the average is meaningful macroscopically. Right, that's an easy one to miss but i don't think that's my problem here. If you are computing enthalpy in another ensemble (which is possible, though it may be harder to interpret) then you would use the average pressure from this quantity I'm running in NPT and was calcaulating H from ave. P, ave. U and ave. V for the run while i understand that this doesn't exactly equal average H it should be close enough for me at this point, going back and redoing it with P set to the reference value (which the average hits with small fluctuations) the resultant H still doesn't line up properly for some example data: pV, g_energyV, m^3 pV, J pV, kJ/mol 442.42 1.46E-26 1.46E-18884.07 P = 1000 bar = 100,000,000 Pa and i see that my pV is around 2x g_energies pV, no values are scaled for the # of items in the box at this point, this is all for moles of the system i think that's alright though You should not use pV from g_energy though, as Michael explained, rather you need ref_p times V. This precludes that your system is in equilibrium of course. -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009062.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] why mass and charge is zero?
On 2013-06-08 17:28, Albert wrote: Hello: I generate a ligand toplogy by ACPYPE with amber GAFF. However, I found that in the ligandGMX.itp file, in the atomtypes section, the mass and charge are all zero, like: [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb NT NT 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 however, in the atoms sections, I found: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 26 NT 1 UKA N10 26-0.719301 14.01000 ; qtot -7.758 I am a little bit confused for this. Does anybody have any idea for it? the ones in the atoms section are the ones that are used UNLESS they are not given, in which case the defaults are used. thank you very much best Albert -- 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
Re: [gmx-users] xx of the xxxx bonded interactions couldn't be calculated
On 2013-06-07 04:12, Justin Lemkul wrote: On 6/6/13 10:00 PM, Badamkhatan wrote: Dear GMX-users Recently i got this error and note from my MD2 simulation. I'm solvating 1-octanol to 1-octanol and calculating free energy differences. This is the last step of my calculation and previous steps are looking fine. Basically i followed Justin's free energy tutorial. Here is Note: A list of missing interactions: LJC Pairs NB of210 missing 1 exclusions of 25308 missing 1 Molecule type '1-octanol' the first 10 missing interactions, except for exclusions: LJC Pairs NB atoms3 25 global 325 Fatal error: 2 of the 57736 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck Please help me and suggest any idea to solve this problem? Sounds like you're http://www.gromacs.org/Documentation/Terminology/Blowing_Up. It may also be the opposite, box shrinking under equilibration. Try: mdrun [options] -rdd 1.25 -Justin -- 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
Re: [gmx-users] ngmx not installed in gmx4.6.1
On 2013-06-04 17:55, Chandan Choudhury wrote: Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. cmake -DGMX_X11=ON Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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
Re: [gmx-users] viscosity
On 2013-06-02 06:40, Marcelo Vanean wrote: *On 2013-06-01 17:11, Marcelo Vanean wrote: * *On 2013-06-01 02:24, Marcelo Vanean wrote: * *Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. * *I used the same energy file (ener.edr) and I get this results: http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. * *Maybe you can post the energy file on that site as well. Have you tried to compute the pressure autocorrelation (using g_energy)?* I didn't the pressure autocorrelation. A question: what does this analysis tell me? Check the equations in the manual and relevant literature. The viscosity is computed from the pressure ACF. I posted the energy file here: http://www.4shared.com/file/SSAU1reN/ener.html. That website does not work. -- 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
Re: [gmx-users] Viscosity
On 2013-06-01 02:24, Marcelo Vanean wrote: Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. Please give some details about your system and how you did the analysis. Did you use the same energy file with the different gromacs versions? In that case they should give the same result. -- 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
Re: [gmx-users] viscosity
On 2013-06-01 17:11, Marcelo Vanean wrote: On 2013-06-01 02:24, Marcelo Vanean wrote: Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. I used the same energy file (ener.edr) and I get this results: http://help-gromacs.blogspot.com.br/. The files visco.xvg are equals. Maybe you can post the energy file on that site as well. Have you tried to compute the pressure autocorrelation (using g_energy)? -- 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
Re: [gmx-users] Dihedral Autocorrelation Function with negative values
On 2013-05-31 15:59, Davide Mercadante wrote: Dear gmx users, I am writing to ask why I am getting a dihedral autocorrelation function (ACF) with negative values. I am trying to calculate the ACF using g_angle (gromacs 4.5.5) with the following set of flags: g_angle -f trajectory.xtc -type dihedral -oc acf.xvg -od angdist.xvg -n angle.ndx The ACF starts from 1 as expected and slowly drops (sometimes) to values below 0 (approx. -0.2). Even when I use the flag -normalize (which I would expect normalizes the ACF between 0 and 1) the output is identical. Can you please help me to figure out why this happens? Any help will be very much appreciated. Thank you in advance. Cheers, David Because the angle between the two planes can become 180 in which case the dot product is negative. In the long run it should go to zero. It is described in D. van der Spoel and H.J.C. Berendsen: Molecular dynamics simulations of Leu-Enkephalin in water and DMSO Biophys. J. 72 pp. 2032-2041 (1997) -- 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
Re: [gmx-users] choice of forcefield
On 2013-05-28 14:39, massimo sandal wrote: What other people do? Read literature. Gromacs allows you to choose many. If you need detailed results use an atomistic force field. 2013/5/28 Dr. Vitaly Chaban vvcha...@gmail.com In my mind, MARTINI is a decent option to build your particular topology upon. Dr. Vitaly Chaban On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker revthi.san...@yahoo.com wrote: Dear all, I am a beginner to performing simulations and my system consists of protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids are in general united atom, while those involving drug-protein systems are all-atom mostly. Kindly suggest me which of these, all-atom or united atom should I be using for my system. Thanks for your help in advance Yours sincerely, Revathi M.S. Research Scholar Indian Institute of Technology,Madras India -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: choice of force field -reg
On 2013-05-28 18:09, Revthi Sanker wrote: Dear Sir, Thank you so much for your reply. To be specific, my system has only four lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was not able to get all atom paramters for these lipids from the lipid book( only united atom parameters were available). So I had resorted to using united atom for the whole system. But I am afraid if I am missing out on some crucial protein-drug interactions because of this united atom consideration. Kindly guide me in this regard. Sorry but you need to check literature and search the web. There are quite some resources out there. You might also look for Jochen Hub's web site. Thank you so much once again. Yours sincerely, Revathi M.S.Research Scholar Indian Institute of Technology Madras India -- 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
Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD
Bond 1539.1181 1539.1162 -0.0019 Angle 3111.9264 3111.9197 -0.0067 Dih 1250.5425 1250.5421 -0.0004 Imp 16.2837 16.2837 0. Coul -1837.8585 -1705.3075 132.5510 LJ -995.0311 -1219.3432 -224.3121 Pot 3084.9904 2993.2110 -91.7794 Something you think is equivalent is not :-) Move to testing a system with two lipids. Inspect all the logfile outputs very carefully for clues. Mark On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 4:19 PM, Reza Salari wrote: Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my systems. My main question is that for the single POPC, all the potential energy terms match very well, but for the membrane system the non-bonding terms differ significantly. I am providing the full details below and greatly appreciate any hint for better comparison of the energies. Thanks, Reza Salari Details: 1) Both systems were prepared using VMD membrane package: 2) It appears you hit send too early. Please provide the entirety of the details you intended. Complete .mdp files and actual quantification of the differences you are observing are also very important. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] Fw: probability from COM of micelle
On 2013-05-09 20:15, Justin Lemkul wrote: On 5/9/13 10:15 AM, mohammad agha wrote: Dear GROMACS Specialist, I want to plot probability (nm^-1) distribution of micelle selected atoms with respect to COM of the micelle (nm). with respect to this definition, Probability was defined as the number of instances the selected atom was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM divided by r, may I ask you to give me one formula to plot of this probability, Please? for example, to plot of density(nm^-3) with respect to COM of micelle (nm), I do as following: density = g(r) * (N/V) It sounds like all you need to do is create a histogram from data produced by g_dist. You can make the histogram with g_analyze or any number of other programs. -Justin How about g_rdf? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Including polarizability by a Drude oscillator or the shell model
On 2013-04-27 19:18, Andrew DeYoung wrote: Hi, I am interested in including polarizability using a Drude harmonic oscillator (charge on a spring). In section 3.5 of the version 4.5.4 manual, Shell molecular dynamics is described briefly. It seems that the shell model is quite similar, if not identical, to the Drude oscillator. However, I do not see in the manual where the use of the shell model in Gromacs simulations is described. Do you know if some sort of tutorial exists about the use of the shell model (or the Drude oscillator) in Gromacs? Thank you so much for your time! Andrew DeYoung Carnegie Mellon University Check here for some examples http://virtualchemistry.org/pol.php -- 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
Re: [gmx-users] Water spreading on graphene!
On 2013-04-20 22:17, sarupria wrote: Dear all, I have a graphene like surface (carbons on a hexagonal lattice with zero partial charges and some LJ parameters) with a drop of water placed on it. In principle, this is a hydrophobic surface and the drop should remain a droplet on it. However, surprisingly I am seeing that the drop is spreading within a 1 ns of the simulation. In the past I have done some similar simulations (with a different structure but basically zero partial charge surface and LJ) on which the drop remains a drop. Does any body have any ideas of what I may be doing wrong? Pasted below is my mdp and top file. Briefly, I am doing NVT simulation, PME for electrostatics, TIP3P water model, the surface is frozen and intra-surface interactions are excluded, the cut-off distances are 1 nm, velocity rescale thermostat (I tried both with the entire system coupled to the same thermostat and with sheet and water being coupled to different thermostats). Any suggestions are welcome. My analysis suggests this comes from the long range electrostatics because we have tested the same thing in LAMMPS. When we turn off PPPM and use cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the software) we don't see the drop spreading. I have done so many simulations and to have this problem stumps me!! Thanks for being helpful always. Interesting, have you tried the cut-off approach in gromacs? Which version are you running by the way? But how can the graphene have partial charge? Or is it terminated with H atoms? You probably should turn off the dispersion correction since this is not a homogeneous system, but that can hardly be the cause. Sapna MDP file Start dt = 0.002; time step nsteps = 100 ; number of steps nstcomm = 10 ; reset c.o.m. motion comm_mode = Linear nstxout = 2000 ; write coords nstvout = 2000 ; write velocities nstlog = 500 ; print to logfile nstenergy = 250 ; print energies xtc_grps= System ; group crds written in xtc nstxtcout = 250 ; freq write xtc files nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME ; algorithm for Coulomb rvdw= 1.00 ; cut-off for vdw rcoulomb= 1.00 ; cut-off for coulomb rlist = 1.00 ; cut-off for nearest neighbor Tcoupl = V-rescale; temp coupling scheme ref_t = 300.0; temp of system tc-grps = System ; system to thermocouple tau_t = 0.5 ; strength of thermocoupling Pcoupl = No ; scheme for pressure coupling Pcoupltype = isotropic; pressure geometry tau_p = 0.5 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; ref pressure DispCorr= EnerPres ; long range correction gen_vel = yes ; generate init. vel gen_temp= 280 ; init. temp. gen_seed= 372340 ; random seed constraints = hbonds ; constraining bonds with H constraint_algorithm = shake freeze_grps = GRO freezedim= Y Y Y energygrps = GRO energygrp_excl = GRO GRO MDP File End # -- View this message in context: http://gromacs.5086.x6.nabble.com/Water-spreading-on-graphene-tp5007497.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] Re: Water spreading on graphene!
On 2013-04-21 12:39, Dr. Vitaly Chaban wrote: Yes, the water droplet should remain a droplet on graphene. Since you have a droplet, I assume you have much vacuum in the system. I would not use PME for such system, but would rather compensate it by using larger cutoffs. It could be an artifact if the box dimension is small compared to the droplet (less than double the droplet size, make it at least three times the droplet). In principle PME should work though. Check the energy before and after the droplet spreads to see whether the energy goes down. If you need a simple advice, it is -- enlarge the box to avoid any interactions, which you would not have had in real experiment. Indeed. I also expect a specific behavior, if your droplet is very small. Maybe, I would simulate this system without PBC at all. Dr. Vitaly Chaban I have a graphene like surface (carbons on a hexagonal lattice with zero partial charges and some LJ parameters) with a drop of water placed on it. In principle, this is a hydrophobic surface and the drop should remain a droplet on it. However, surprisingly I am seeing that the drop is spreading within a 1 ns of the simulation. In the past I have done some similar simulations (with a different structure but basically zero partial charge surface and LJ) on which the drop remains a drop. Does any body have any ideas of what I may be doing wrong? Pasted below is my mdp and top file. Briefly, I am doing NVT simulation, PME for electrostatics, TIP3P water model, the surface is frozen and intra-surface interactions are excluded, the cut-off distances are 1 nm, velocity rescale thermostat (I tried both with the entire system coupled to the same thermostat and with sheet and water being coupled to different thermostats). Any suggestions are welcome. My analysis suggests this comes from the long range electrostatics because we have tested the same thing in LAMMPS. When we turn off PPPM and use cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the software) we don't see the drop spreading. I have done so many simulations and to have this problem stumps me!! Thanks for being helpful always. -- 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
Re: [gmx-users] Re: Water spreading on graphene!
On 2013-04-21 18:25, Sapna Sarupria wrote: Dear David and all, Thanks for the suggestions! I did increase the box size to twice that of the sheet dimensions. The sheet is 10 x 10 nm^2 and now is place in the center of a 20 x 20 x 20 nm^3 box with the droplet size of about 5 nm (4142 water molecules). I still see the droplet spreading. I will check the energies and also attempt the simulation with the cut-off distances. May be that will help. However, in a silica surface with no surface charges the drop remains a drop (as expected). I use the same mdp files for both the simulations. You did not explain the charges on graphene. Sapna On Sun, Apr 21, 2013 at 12:14 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-04-21 12:39, Dr. Vitaly Chaban wrote: Yes, the water droplet should remain a droplet on graphene. Since you have a droplet, I assume you have much vacuum in the system. I would not use PME for such system, but would rather compensate it by using larger cutoffs. It could be an artifact if the box dimension is small compared to the droplet (less than double the droplet size, make it at least three times the droplet). In principle PME should work though. Check the energy before and after the droplet spreads to see whether the energy goes down. If you need a simple advice, it is -- enlarge the box to avoid any interactions, which you would not have had in real experiment. Indeed. I also expect a specific behavior, if your droplet is very small. Maybe, I would simulate this system without PBC at all. Dr. Vitaly Chaban -- 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
Re: [gmx-users] pdb2gmx for small molecules?
On 2013-04-18 21:35, Justin Lemkul wrote: On 4/18/13 3:32 PM, Warren Gallin wrote: Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling non-protein/nucleic acid as input. I have created a pdb file for my molecule of interest, but when I invoke pdb2gmx as follows: pdb2gmx -f BrMT_mono_nores.pdb -water tip4 I get a Fatal error message because there is no residue name (it's neither protein or nucleic acid): --- Program pdb2gmx, VERSION 4.5.4 Source code file: /Users/wgallin/Desktop/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue '' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and just above that message there is also a Warning in the message saying: Warning: Starting residue 1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Is there some documentation that specifically addresses the methods and issues with using pdb2gmx for non-protein/nucleic acid molecules? pdb2gmx only knows how to handle what it knows about. There is no generic support for arbitrary compounds. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin Try GAFF using the Ambertools and acpype. -- 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
Re: [gmx-users] Re: thermal conductivity,specific heat,enthalpy
On 2013-04-11 22:20, Ahmet yıldırım wrote: could anybody help me please? Check http://pubs.acs.org/doi/abs/10.1021/ct200731v 2013/4/11 Ahmet yıldırım ahmedo...@gmail.com Dear users, I calculated diffusion constant of a substance using g_msd tool. I also want to calculate thermal conductivity its. By the way,I did npt simulation. Diffusion constant=alpha Thermal conductivity=k specific heat=Cp density=d alpha=k/(d.Cp) and k=alpha.d.Cp I need d and Cp to calculate k. 1.) To calculate Cp: Prof. Spoel:From http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html cP = (H^2 - H^2)/kB T^2 (NPT sim) The .edr file gives average enthalpy H. According to above formula, I need both H and H. How can I get H (not average)? 2.) .edr file: 1 LJ-(SR) 2 LJ-(LR) 3 Coulomb-(SR) 4 Coul.-recip. 5 Potential6 Kinetic-En. 7 Total-Energy 8 Temperature 9 Pressure10 Box-X 11 Box-Y 12 Box-Z 13 Volume 14 Density 15 pV 16 Enthalpy 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 Mu-X 37 Mu-Y38 Mu-Z39 T-System40 Lamb-System Firstly I calculated Entalphy (16) Afterward I calculated both Etot (7) and pV (15) Enthalpy=Etot+pV Unfortunately, I get Enthalpy isnt equals to Etot+pV. Why? -- Ahmet Yıldırım -- 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
Re: [gmx-users] Dihedral angle PCA
On 2013-04-10 08:33, anu chandra wrote: Dear Gromacs users, I would like to do side-chain dihedral angle PCA for my protein. The protein contains 293 residues. I came across an explanation about dihedral PCA in gromcas website ( http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA). Is it possible to do side-chain dihedral PCA using the same methodology? Is there any other programmes anyone came across for side-chain dihedral PCA? Waiting for your valuable reply. Thanks in advance Regards Anu Have you tried following the steps there? I think it should work. Other than that dihedral PCA is regarded as not very useful by at least some people because it is difficult to interpret the results in structural terms. For instance maxima in a multidimensional torsional energy landscape may be due to atoms coming close (hence preventing the sampling) without giving any real information on the structures. But this is for you to decide :). -- 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
Re: [gmx-users] Normal Mode Analysis -- Expected Output
On 2013-04-11 17:57, Bryan Roessler wrote: Hello, I am running a normal mode analysis on a ~1500AA protein with the following mdp parameters: Log file opened on Tue Apr 9 09:55:00 2013 Host: uv1 pid: 128985 nodeid: 0 nnodes: 64 Gromacs version:VERSION 4.6.1 Precision: double Memory model: 64 bit MPI library:MPI OpenMP support: disabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Fri Mar 15 09:20:59 CDT 2013 Built by: asndcy@uv [CMAKE] Build OS/arch: Linux 3.0.58-0.6.6-default x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2667 0 @ 2.90GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /opt/sgi/mpt/mpt-2.07/bin/mpicc GNU gcc (GCC) 4.7.2 C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG :-) G R O M A C S (-: Good gRace! Old Maple Actually Chews Slate :-) VERSION 4.6.1 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) /opt/asn/apps/gromacs_4.6.1/bin/mdrun_mpi_d (double precision) (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- Changing rlist from 1.47 to 1.4 for non-bonded 4x4 atom kernels Input Parameters: integrator = nm nsteps = 10 init-step= 0 cutoff-scheme= Verlet ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 100 comm-mode= Linear nstlog = 1000 nstxout = 500 nstvout = 500 nstfout = 500 nstcalcenergy= 100 nstenergy= 500 nstxtcout= 0 init-t = 0 delta-t = 0.002 xtcprec = 1000 fourierspacing = 0.12 nkx = 160 nky = 160 nkz = 216 pme-order= 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface = 0 optimize-fft = TRUE ePBC = xyz bPeriodicMols= FALSE bContinuation= FALSE bShakeSOR= FALSE etc = No bPrintNHChains = FALSE nsttcouple = -1 epc = No epctype = Isotropic
Re: [gmx-users] Memory requirement to store trajectories
On 2013-04-11 20:30, Sikandar Mashayak wrote: Hi I would like to determine an estimate of hard disk space required to perform a typical MD simulation using gromacs. To do so, I am thinking of first finding how many bytes are required to store single atom's position, velocity and force in .trr file for a single frame, and then determine total bytes required by multiplying it by total number of atoms and required number of time-frames for a given system. So, can anyone give me an estimate of number of bytes required to store single atom's position, velocity and force in .trr file of gromacs? Also please suggest me if there is any other better approach to determine an estimate of hard disk space required. Thanks Sikandar grompp prints it for you if it is more than a certain amount (2 Gb I think). -- 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
Re: [gmx-users] GROMACS 4.6 with GPU acceleration (double presion)
On 2013-04-09 18:06, Mikhail Stukan wrote: Dear experts, I have the following question. I am trying to compile GROMACS 4.6.1 with GPU acceleration and have the following diagnostics: # cmake .. -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DCUDA_HOST_COMPILER=/usr/bin/gcc -DCUDA_PROPAGATE_HOST_FLAGS=OFF CMake Error at cmake/gmxManageGPU.cmake:46 (message): GPU acceleration is not available in double precision! Call Stack (most recent call first): CMakeLists.txt:143 (include) Are there any plans to have double precision with GPU acceleration in the coming version of GROMACS or this will not happen in the nearest future. The hardware does not support it yet AFAIK. Thanks and regards, Mikhail -- 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
Re: [gmx-users] Lipids and virtual site in 4.6.1
On 2013-04-08 11:34, Bastien Loubet wrote: Dear GROMACS user, Last week I was watching the GTC talk from Eric Lindahl, and I noticed his insistence on virtual site to accelerate simulation (up to 5ps time step). As a matter of fact our group recently tried to use virtual site on CHARMM36 POPC bilayer and the result where less than stellar. We first did a simulation of a POPC bilayer comparing area per lipid with and without virtual site using GROMACS 4.5.5. We obtained an area per lipid around 0.62 nm^2 per lipid with no virtual site but with virtual site we obtained an area per lipid of more than 0.7 nm^2. After that we found that there was a bug report for the virial calculation with virtual site in version 4.5: http://redmine.gromacs.org/issues/908 The issue being marked as resolved for 4.6 and we tried our hand at both the beta3 and 4.6.1 version of it. The result where better but not perfect: we get 0.65~0.66 nm^2 per lipid. The problem here is that in order to increase the time step we need all hydrogen to be virtual sites, so this include the lipids hydrogen and not just the protein. However if the area per lipid is wrong the stress profile is likely to be changed, which will affect transmembrane proteins. So we do not feel confident about using virtual sites in our lipid simulation. I signal it here because there is a possibility that this is still a bug, If somebody could confirm/infirm that it would be nice. Did you also try to use vsites without increasing the time step, in order to rule out that this is a time step effect rather than a vsite effect? Best, Bastien -- View this message in context: http://gromacs.5086.n6.nabble.com/Lipids-and-virtual-site-in-4-6-1-tp5007063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] Lipids and virtual site in 4.6.1
On 2013-04-08 11:52, David van der Spoel wrote: On 2013-04-08 11:34, Bastien Loubet wrote: Dear GROMACS user, Last week I was watching the GTC talk from Eric Lindahl, and I noticed his insistence on virtual site to accelerate simulation (up to 5ps time step). As a matter of fact our group recently tried to use virtual site on CHARMM36 POPC bilayer and the result where less than stellar. We first did a simulation of a POPC bilayer comparing area per lipid with and without virtual site using GROMACS 4.5.5. We obtained an area per lipid around 0.62 nm^2 per lipid with no virtual site but with virtual site we obtained an area per lipid of more than 0.7 nm^2. After that we found that there was a bug report for the virial calculation with virtual site in version 4.5: http://redmine.gromacs.org/issues/908 The issue being marked as resolved for 4.6 and we tried our hand at both the beta3 and 4.6.1 version of it. The result where better but not perfect: we get 0.65~0.66 nm^2 per lipid. The problem here is that in order to increase the time step we need all hydrogen to be virtual sites, so this include the lipids hydrogen and not just the protein. However if the area per lipid is wrong the stress profile is likely to be changed, which will affect transmembrane proteins. So we do not feel confident about using virtual sites in our lipid simulation. I signal it here because there is a possibility that this is still a bug, If somebody could confirm/infirm that it would be nice. Did you also try to use vsites without increasing the time step, in order to rule out that this is a time step effect rather than a vsite effect? And by the way, you are welcome to reopen the redmine issue and upload file demonstrating the problem. Best, Bastien -- View this message in context: http://gromacs.5086.n6.nabble.com/Lipids-and-virtual-site-in-4-6-1-tp5007063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] Free energy landscape by g_sham
On 2013-03-31 12:21, Kavyashree M wrote: Thank you Sir Note that the free energy differences are rigorously correct only if the array of the cells in the grid correspond units of phase space with the same volume. This is close to impossible to achieve, but the plots may still give insight. Regards kavya On Sun, Mar 31, 2013 at 11:58 AM, bipin singh bipinel...@gmail.com wrote: g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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 -- --- Thanks and Regards, Bipin Singh -- 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 -- 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: diffusion constant level off
On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I have strange Diffusion results (especially 10,50,100,150,200 ns). How can I fix this problem? Results: Time (ns) D(cm^2/s) 10 0.1616 20 0.0735 30 0.0775 40 0.1097 50 0.1471 60 0.0468 70 0.0667 80 0.0727 90 0.0664 100 0.1336 110 0.0899 120 0.0572 130 0.0506 140 0.0723 150 0.1466 160 0.0703 170 0.081 180 0.0278 190 0.1121 200 0.3136 2013/3/27 Ahmet yıldırım ahmedo...@gmail.com Dear users, I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius of gyration, RMSD matrix. This simulation has reached to converge at last 50 ns. g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1 g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 ... g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 1.) I used the above commands without the following flags ( -type, -lateral and -ten). Which diffusion will the above comands give? is it bulk diffusion? Gromacs manual: -type:Compute diffusion coefficient in one direction:no, x, y or z -lateral:Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z -ten:Calculate the full tensor 2.) I plotted diffusions (10 values) as function of time. Diffusions dont converge. Did I do any steps by mistake? 3.) From manual: The diffusion constant is calculated by least squares fitting a straight line (D*t + c)... What is (D*t + c)? What are the meaning of D and c? 4.) What should be Time between restarting points in trajectory? Thanks in advance -- Ahmet Yıldırım -- Ahmet Yıldırım -- 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
Re: [gmx-users] How to specify water molecules number added to box?
On 2013-03-24 09:23, ca...@mail.ustc.edu.cn wrote: Dear all, I am new to gromacs. I would like to add water molecules of specific number into my systems. As I found no answer out of the manual, I have to ask you for help. How can I specify water molecules number (like 484 water molecules) added into my system. Does it has anything with -ci and -nmol options of the program genbox? Your reply would be appreciated. genbox -h try -maxsol Thanks, Zhikun, from USTC -- 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
Re: [gmx-users] Treating electrostatics and van der Waals interactions differently
On 2013-03-15 19:27, Jeff Woodford wrote: Hi all, I am attempting to simulate a system that has strong ionic character so I would like to treat the electrostatics and van der Waals interactions separately. For example I would like to include all pairs of atoms in the electrostatics calculation but I would like to exclude 1-2 and 1-3 neighbors in the van der Waals calculation. Is this possible to do in GROMACS? If so, how might this be accomplished? Thanks in advance for your help. Jeff Woodford Assistant Professor of Chemistry Missouri Western State University In a molecular system you can do this by adding the 1-2 and 1-3 interactions as pairs, assuming the list of interactions is fixed, like in a crystal. Then you can make the LJ parameters different from the default and scale the charges down. You probably want to use PME for electrostatics. Check the manual! -- 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
Re: [gmx-users] Dihedral restraints in 4.6 vs 4.5.X
On 2013-03-15 15:31, Per Larsson wrote: Hi I anyone aware of any issue starting simulations with 4.6 (or 4.6.1) from a 4.5.X-tpr file with dihedral restraints? I'm unsuccessful in making them start. To investigate further, I created a small dialanine peptide in vacuum, with a dihedral restraint. Here's the details: Making a 4.5.5 tpr with a dihedral restraint $grompp -f md.mdp -c conf.gro -p topol.top -o md.tpr Checking that it is there: $gmxdump -s md.tpr |grep DIHRE Reading file md.tpr, VERSION 4.5.5 (single precision) functype[166]=DIHRES, label=0, power= 1 phi= 1.2000e+02, dphi= 3.e+01, kfac= 1.e+00) Now running this in 4.5.5 works fine, but starting it in 4.6 (or 4.6.1) gives me an error. $ /Users/per/source/gromacs-4.6.1/build/src/kernel/mdrun -v -deffnm md Reading file md.tpr, VERSION 4.5.5 (single precision) --- Program mdrun, VERSION 4.6.1 Source code file: /Users/per/source/gromacs-4.6.1/src/gmxlib/symtab.c, line: 136 Fatal error: symtab get_symtab_handle 1051260126 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Taking away the restraint allows me to start the run in 4.6.1, and also reformatting the [ dihedral_restraint ] section to comply with 4.6 works. Is this a know issue, am I missing something obvious, or should I file an issue on redmine? redmine please. Thanks /Per-- 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 -- 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] Fwd: [gmx-developers] Simulated annealing problem
This is a user problem, not a development problem. Original Message Subject: [gmx-developers] Simulated annealing problem Date: Thu, 14 Mar 2013 10:15:39 +0530 From: Gaurav Jerath g.jer...@iitg.ernet.in Reply-To: Discussion list for GROMACS development gmx-develop...@gromacs.org To: gmx-develop...@gromacs.org Hi, I am trying to anneal two protein molecules. The usual protocol for a MD simulation was followed. But the problem arises that at high temperatures, the number of hydrogen bonds are increasing instead of getting decreased. The GROMOS43a1 force field was used and the mdp file for the simulation is shown below: ; title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002;ps ! nsteps = 500 ; total 10ns. ;nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein non-Protein; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300 300 ; reference temperature, one for each group, in K ; Energy monitoring energygrps = Protein SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 2.75 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 310 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 ; SIMULATED ANNEALING CONTROL = annealing = periodic periodic annealing_npoints= 3 3 annealing_time = 0 5000 1 0 5000 1 annealing_temp = 300 500 300 300 500 300 Kindly help me as I am unable to figure out if there is a problem in my parameters file -- gmx-developers mailing list gmx-develop...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-developers Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-requ...@gromacs.org. -- 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] Postdoc jobs developing gromacs etc.
If you are interested in a gromacs-related development position at the postdoc level, please have a look at our ad below. Please spread to interested colleagues. http://www.uu.se/jobb/others/annonsvisning?languageId=1tarContentId=235221 Regards, -- 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
Re: [gmx-users] Small bug with -pi in g_mindist?
On 2013-03-07 19:02, Reid Van Lehn wrote: Hi users, I was experimenting with using a hexagonal unit cell for a lipid membrane system by building a box with vectors A A C (i.e. two equivalent vectors in the xy plane and distinct z vector) and angles 90 90 60, which is correctly represented as hexagonal after converting with trjconv. I equilibrated this box and a system with the same number of lipids and water molecules but in a rectangular box. I confirmed that after equilibration the area per lipid for each system is the same, and after visualization confirmed that the hexagonal system and rectangular system occupied about the same area (of course subject to fluctuations). For a hexagon and square of equivalent area, the minimum distance between periodic images should be 1/sqrt( sin 60 degrees) = ~1.075 times larger for the hexagon than in the square case if I worked out the geometry correctly. To test to make sure I had the correct new minimum distance, I ran g_mindist -pi with both a single atom and a single water molecule from the simulation box after resizing the Z axis to a large value, restricting the minimum distance between periodic images to only the xy plane. Surprisingly, the result came out as smaller than the equivalent minimum distance in the rectangular box, and was equal to the box vector B. Since in GMX box vectors are stored in the .gro file in a 3x3 matrix, the box[YY][YY] vector for an ab angle of 60 degrees was (correctly) equal to sin 60 * the A vector. However, the correct periodic distance should have been the A vector, which again was correctly ~1.075 * the box vector in the rectangular box by comparing the .gro files. I believe that this is a small bug in g_mindist, and found the source: on lines 71 and 92 of gmx_mindist.c (version 4.6), the initial minimum distance is set based on the minimum of the box[XX][XX], box[YY][YY], and box[ZZ][ZZ] vectors. I think this is fine for rectangular boxes, but fails for triclinic boxes with box angles differing from 90 degrees. In my particular case of a hexagonal xy plane, the box[YY][YY] vector is shorter than the box[XX][XX] vector by a factor of sin 60, but this is not actual the shortest distance. Explicitly printing out the distances calculated between periodic images in the current version of the code for both a single atom and a water molecule confirms that the minimum distance is the box[XX][XX] vector. Thanks for reporting and giving a solution. http://redmine.gromacs.org/issues/1183 A fix for this was substituting norm(box[0]), norm(box[1]), and norm(box[2]) for the box[XX][XX] etc. vectors in line 71, as then the minimum was properly set. I realize this is a bug that is unlikely to affect many users, but given the prevalence of non-rectangular boxes and the observation of previous complaints about mindist in the user list, I thought it would be good to report. Please let me know if I made an error anywhere! Best, Reid -- 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
Re: [gmx-users] Whether CHARMM force field in GROMACS is different from that in CHARMM commercial package
On 2013-02-14 07:02, fayaz wrote: Dear Gromacs Forum, I want to do RNA simulation using Gromacs. I have installed gromacs 4.5.5 and i found Charmm force field present in it. Can I use this force field for my simulation. I am asking this because I heard that Charmm force field in Gromacs is incomplete and different from the one that is present in CHARMM software package. I think this conception is present with many of the gromacs users. Most of my friends are also not using Charmm force field that comes with gromacs. Please clear this doubt. Please read the paper by Bjelkmar et al. about the implementation of the FF. Rumors is not enough, but if there is concrete evidence that something is incorrect a bug-report should be filed at http://redmine.gromacs.org. Another question is whether Amber or Charmm is the better force field for RNA. In my group we use Amber. Thanks in advance Fayaz -- View this message in context: http://gromacs.5086.n6.nabble.com/Whether-CHARMM-force-field-in-GROMACS-is-different-from-that-in-CHARMM-commercial-package-tp5005524.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] Water models and diffusion coefficient
On 2013-02-09 14:21, Joinforfun Doe wrote: Hello, I am simulating a model of heavy water, with charges modified from SPCE model. This was proposed by Grigera [2001], with H replaced by D and charges on O and H increased from values proposed in SPCE model. I have verified by using gmxdump that gromacs sees the mass of H as 2.014 amu and the charges as specified in the topology file. The density comes out as expected for heavy water. The system equilibrates well (well-defined fluctutations, no trends in energy, density, pressure, temperature) However, the diffusion coefficient is always lower than that expected for the model. By using the same parameter files I ran a simulation for normal water (SPCE) model and the diffusion coefficient matches with that reported from other simulations. Is there something else that I should check? or is there something about g_msd that I am missing? Any pointers would be really helpful. Thanks Most water models have too high D. (see J Chem Phys 108 pp. 10220-10230 (1998)). SPC/E is about right. However that is more luck than skill so to speak, since there still is a lot of physics missing from this extremely simple model. So if you can reproduce literature values for the model and some experimental data, dens, DHvap, then this is as good as it gets. -- 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
Re: [gmx-users] Re: Water models and diffusion coefficient
On 2013-02-09 19:26, learnmd wrote: For a simulation that is 300 ns long (after NVT and NPT equilibration steps of 1 ns each), I am saving output every 2 ps. The time step is 2 fs. nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps Is that saving data too rarely? No but check the flags in g_msd. Try without restarting, that is -trestart 31. Thanks, -- View this message in context: http://gromacs.5086.n6.nabble.com/Water-models-and-diffusion-coefficient-tp5005377p5005385.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] get the center of a cluster using gromacs
On 2013-02-01 16:14, Houcemeddine Othman wrote: Hi, I used this command g_cluster -f input.pdb -s input.pdb -cl output.pdb -nofit -av I got a file containing all the structures of the cluster. I am not sure if the first one is the cluster center? It says in the cluster.log file. Houcemeddine On Mon, Jan 28, 2013 at 9:49 AM, francesco oteri francesco.ot...@gmail.comwrote: Hi, you can try using g_cluster, taking care to use the option -cl Francesco 2013/1/28 Houcemeddine Othman houce...@gmail.com Hi, How can I get the center of a cluster from a multiple conformers pdb file (a file containing a cluster of a docking poses). I tried to use g_covar to get an average structure but I get a distorted structure when averaging over the whole atoms of the protein. -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in BlueGene
/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 -- 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_x2top is missing bonds
On 2013-01-31 22:55, FX wrote: Hey Matt, (It's a small world, eh?) I don't have a particular reason to use Gromacs. I used it for small ions solvation ten years back, I liked it, but every time I have tried to use it since for crystalline systems, I was put off because, as you say, it's probably not what it's designed for. In that particular case, I set out to use Gromacs because I'm working to reproduce a published paper that used Gromacs. Anyway, I'm interested in this new thread development (and suggestions as to alternatives more suited to my system), but also in suggestions regarding my original question :) Cheers, FX-- 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 try acpype iso g_x2top (this comes straight from the developer). -- 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
Re: [gmx-users] gromacs 4.6 GB/SA problem and poor performance
On 2013-01-21 09:55, Changwon Yang wrote: Im trying to run an md or em using an implicit solvation method using gromacs 4.6 but I always get the incorrect result. ICC version : icc 11.0 fftw version : 3.2.2 benchmark system is gromacs-gpubench gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench Angle,Proper Dih,Imp Dih,Nonpolar sol,LJ-14,Coulomb-14 energy are correct. but GB polarization energy is too low, LJ(SR),Coulomb(SR) energy are always zero. It seems that there is a bug in the program. Using gromacs 4.5. It works fine. gromacs 4.5.3 : 9.4ns/day gromacs 4.6 :2.4ns/day Can you please file a redmine issue with sample input files? http://redmine.gromacs.org Thanks! -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-4-6-GB-SA-problem-and-poor-performance-tp5004728.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] how to convert a dodecahedric trajectory into a triclinic one?
On 2013-01-16 16:03, Anna Marabotti wrote: Dear All, I performed a MD simulation of a protein into a rhombic dodecahedric box. Now I'd need to convert this dodecahedric box into a triclinic one (I mean, not only for one frame to obtain a .gro file, but for the entire trajectory). I think that it would be possible using trjconv command, but I have some trouble in doing it, I don't understand which are the correct flags to use. Could anybody give me some suggestion about this problem? Many thanks in advance and best regards Anna It already is a triclinic box. You don't have to do anything. -- 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
Re: [gmx-users] how to indicate solvent flexibility?
On 2013-01-10 10:45, Albert wrote: Hello Justin and Leandro: thanks a lot for kind advices. I am trying to us the g_msd to calculate the density: try g_msd -h wrong tool. first I made a index file called density.ndx with g_select, defined the solvent within 6A of a residue after that I try to run g_msd with command: g_msd_mpi -f md.xtc -s analysis.tpr -n density.ndx -mol diff_mol.xvg -o msd.xvg a dialoug popped up with above command: . Group 13963 (close_27926.000) has 7 elements Group 13964 (close_27928.000) has 5 elements Group 13965 (close_27930.000) has 7 elements Group 13966 (close_27932.000) has 7 elements Group 13967 (close_27934.000) has 7 elements Group 13968 (close_27936.000) has 8 elements Group 13969 (close_27938.000) has 9 elements Group 13970 (close_27940.000) has 6 elements Group 13971 (close_27942.000) has 9 elements Group 13972 (close_27944.000) has 9 elements Group 13973 (close_27946.000) has 9 elements Group 13974 (close_27948.000) has10 elements Group 13975 (close_27950.000) has 9 elements Group 13976 (close_27952.000) has12 elements Group 13977 (close_27954.000) has10 elements Group 13978 (close_27956.000) has 9 elements Group 13979 (close_27958.000) has10 elements Group 13980 (close_27960.000) has 8 elements Group 13981 (close_27962.000) has10 elements Group 13982 (close_27964.000) has10 elements Group 13983 (close_27966.000) has 7 elements Group 13984 (close_27968.000) has 9 elements Group 13985 (close_27970.000) has 8 elements Group 13986 (close_27972.000) has 8 elements Group 13987 (close_27974.000) has 7 elements Group 13988 (close_27976.000) has 9 elements Group 13989 (close_27978.000) has 6 elements Group 13990 (close_27980.000) has 9 elements Group 13991 (close_27982.000) has 8 elements Group 13992 (close_27984.000) has 8 elements Group 13993 (close_27986.000) has11 elements Group 13994 (close_27988.000) has10 elements Group 13995 (close_27990.000) has11 elements Group 13996 (close_27992.000) has10 elements Group 13997 (close_27994.000) has11 elements Group 13998 (close_27996.000) has11 elements Group 13999 (close_27998.000) has 9 elements Group 14000 (close_28000.000) has12 elements I select 14000 which is the last one, but it failed with messages: rogram g_msd_mpi, VERSION 4.5.5-dev-20121121-3e633d4 Source code file: /home/albert/software/gromacs/src/tools/gmx_msd.c, line: 739 Fatal error: The index group does not consist of whole molecules For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Can't You Make This Thing Go Faster ? (Black Crowes) thank you very much Albert On 01/08/2013 06:15 PM, Justin Lemkul wrote: On 1/8/13 11:42 AM, Albert wrote: hello: I've finished a 60ns MD simulation with Gromacs and I found that the flixbility of solvent molecules inside the protein is different when it binds with different ligands: ie. in one case the solvent can move very fast with bulk environment, and in other case the solvent forms type Hbonds with resdiues inside protein. I am just wondering how which module of Gromacs can I use to indicate the solvent difference in flexibility? Is it possible to calculate the entropy in certain region (let's say: 20Z30 ) of the solvent? It sounds like g_rmsf and g_msd may be useful here. The only way to specify geometric criteria for index groups is to use g_select, but then the analysis has to be done on each individual frame, not the trajectory. Dynamic selections will be more conveniently implemented in a future Gromacs version. -Justin -- 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
Re: [gmx-users] Toy input system - MD simulation
On 2013-01-09 12:25, Maria Astón Serrano wrote: Hello, I am new at this and I am working with the constraints algorithms used in a MD simulation. I would like to now how they work, what type of coordinates they use and also to identify some variables. For that, I am trying to do a simulation with a toy input system, like methane or ethane but I am having some troubles: I started with a methane PDB file and pdb2gmx but I got errors, I tried with a ethane simulation using the files: ethane.gro, ethane.mdp and ethane.top but I also got errors, ... I know it is a very open-question but, could you help me? What would you recommend me? Do you have a toy input system? Thank you very much, Maria http://virtualchemistry.org -- 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
Re: [gmx-users] how to convert CGenFF into .itp file?
On 2012-12-26 13:00, Albert wrote: On 12/26/2012 12:39 PM, Peter C. Lai wrote: It should come with two files. A .prm file, which contains the actual forcefield parameters that you use the script to convert to bonded and nonbonded .itp and atomtypes.atp The .rtf file is the charmm equivalent of our .rtp file: it contains some premade residue topologies with charge and connectivity information. I don't know if there are scripts to convert this or not, but it's easy enough to get what you need by hand especially since if your ligand isn't in there, you'll have to create the .rtp entry on your own or get them from paramchem anyway... THX for comments. It works now and I get a folder called cgenff-2b7.ff like what we seen in the share/top folder for other FF. that's too complicated to real use. Initially, I thought that the output for the ligand should be a single .itp file like what we found in Swissparam. Probably one can consider improve this script. As far as I know the CGenFF website can export full parameters for the ligand even it is already exist in CGenFF off line files. In this cases, the output file fro CGenFF website is independent from the offline FF and it already has complete necessary information for paramters and topology). Probably one can consider improve this script and export the output file as a single .itp file. Hey, it's open source. Let us know how it goes :). best Albert -- 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
Re: [gmx-users] how to convert CGenFF into .itp file?
On 2012-12-26 20:29, Albert wrote: On 12/26/2012 07:53 PM, David van der Spoel wrote: Hey, it's open source. Let us know how it goes Sorry what I meant was: If you make a better version of the charmm2gromacs script, then please upload it to the website. Cheers, David. you can simple create an account and login https://www.paramchem.org/ after your login, click upload molecule in left panel. Now you will see the option: Include parameters that are already in CGenFF tick this option and the server will generate a full version of ligand topology which could be independent from the offline CGenFF. Now what we need is just improve the script and convert it into a single .itp file into Gromacs. I think this would be the best solution. Here is an example output for Methanol molecule from CGenFF --example-- * Toppar stream file generated by * CHARMM General Force Field (CGenFF) program version 0.9.6 beta * For use with CGenFF version 2b7 * read rtf card append * Topologies generated by * CHARMM General Force Field (CGenFF) program version 0.9.6 beta * 36 1 ! penalty is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. RESI 8870.000 ! param penalty= 0.000 ; charge penalty= 0.000 GROUP! CHARGE CH_PENALTY ATOM O OG311 -0.651 !0.000 ATOM C CG331 -0.039 !0.000 ATOM H1 HGA30.090 !0.000 ATOM H2 HGA30.090 !0.000 ATOM H3 HGA30.090 !0.000 ATOM H4 HGP10.420 !0.000 BOND OC BOND OH4 BOND CH1 BOND CH2 BOND CH3 END read param card flex append * Parameters generated by analogy by * CHARMM General Force Field (CGenFF) program version 0.9.6 beta * ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. BONDS CG331 OG311 428.00 1.4200 ! PROT methanol vib fit EMB 11/21/89 CG331 HGA3322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 OG311 HGP1545.00 0.9600 ! PROT EMB 11/21/89 methanol vib fit; og tested on MeOH EtOH,... ANGLES OG311 CG331 HGA3 45.90108.89 ! PROT MeOH, EMB, 10/10/89 HGA3 CG331 HGA3 35.50108.405.40 1.80200 ! PROT alkane update, adm jr., 3/2/92 CG331 OG311 HGP1 57.50106.00 ! Team Sugar, HCP1M OC311M CC331M; unchanged DIHEDRALS HGA3 CG331 OG311 HGP1 0.1800 3 0.00 ! og methanol IMPROPERS END RETURN -- 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
Re: [gmx-users] Box Pressure on individual box walls
On 2012-12-16 21:09, John Doe wrote: Hello All, I was wondering if it's possible to get the pressure on individual walls of a pbc cubic box. I specifically want the pressure on the walls perpendicular to the x, y, z axis. g_energy will do it. Thank you for your time. -- 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 -- 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 to run charmm2gromacs-pvm.py correctly?
On 2012-11-27 17:58, Albert wrote: Hello: I am trying to convert the output from CGenFF website into Gromacs .itp format by command: python charmm2gromacs-pvm.py charmm.rst you need an extra file. IIRC the cgenff method gives you two files. but it said: Traceback (most recent call last): File charmm2gromacs-pvm.py, line 33, in module parFile = open(sys.argv[2], 'r') IndexError: list index out of range I open the script, it said: inparameters: command line parameters: 1charmm topology file 2corresponding charmm parameter file 3optfoldername, default cgenff.ff outfiles: 1foldername/atomtypes.atp 2foldername/forcefield.itp 3foldername/forcefield.doc 4foldername/aminoacids.rtp 5foldername/ffbonded.itp 6foldername/ffnonbonded.itp 7foldername/forcefield.r2b 8optfoldername/lipids.rtp(if '!lipid section' statement in CHARMM top file) 9optfoldername/cmap.itp(if genCMAP = True) It seems that the input file is a folder instead of a single file? I generate my ligand topology from the CGenFF website and I only get a .rst file THX -- 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
Re: [gmx-users] where is the script?
On 2012-11-26 12:00, Albert wrote: Hello: I found that someone mentioned that there is a script from Mark which could be used to convert CGenff format into Gromacs .itp file. I searched the mailist and didn't find it. I am just wondering where can I obtain this script? thank you very much best Albert It's posted on the website. http://www.gromacs.org/Downloads/User_contributions/Other_software You want this one: charmm2gromacs-pvm.py -- 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
Re: [gmx-users] How to avoid adding ions close to ligand
On 2012-11-26 21:28, Yun Shi wrote: Hi everyone, I am doing conventional MD of a protein-ligand system with a mobile loop as part of the binding site. Presumably, the positive Arg side chain on the mobile loop will eventually move towards the negative carboxylic group on my ligand. But I found the addition of NaCl (0.15 M conc.) had some effect on this movement, since the random addition could put Na+ or Cl- ions between the mobile loop and my ligand. I tried generating a index containing only SOL far not close to my ligand, but apparently genion requires a continuous solvent group. So is there any other way to achieve this? Trying different numbers for -seed option seems inefficient and is dependent on luck. Thanks, Yun Maybe your assumption is wrong? Run a long MD simulation and you will find out. -- 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
Re: [gmx-users] Different average H bonds with different g_hbond releases
On 2012-11-24 05:41, Acoot Brett wrote: If we got the results by 4.5.4, what will be the method to analyze it by 4.5.5? By a pathch or by installation of 4.5.5 to analyze the 4.5.4 results? In practice there is no problem to have a number of gromacs versions installed. It is typically not recommended to switch gromacs versions of mdrun during a project - unless there are know issues - but for the analysis this is less critical. In this case 4.5.5 should be used. Cheers, Acoot --- On Sat, 24/11/12, Justin Lemkul jalem...@vt.edu wrote: From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Different average H bonds with different g_hbond releases To: Discussion list for GROMACS users gmx-users@gromacs.org Received: Saturday, 24 November, 2012, 9:30 AM On 11/23/12 5:23 PM, Luigi CAVALLO wrote: Hi, we have a .xtc and .tpr file. We were interested in the average number of H-bonds in the last 10ns of a 60ns long trajectory. We analyzed the jobs as g_hbond -f traj1_0-60ns.xtc -s topol.tpr -b 5 -num hbond.xvg. We are displaced by having a different number depending on the g_hbond release. Release 4.5.4 : Average number of hbonds per timeframe 163.620 out of 118112 possible Release 4.5.5 : Average number of hbonds per timeframe 168.168 out of 118112 possible Looking at the hbond.xvg file, the number of H-bonds in each frame are clearly different between the two releases. How is this possible ? We checked single versus double precision g_hbonds, same behavior. We checked that the initial part of the output, i.e. all the various g_hbond defaults, they are the same. We tested different computers and compilations, same behavior. The topology and the md run were done with release 4.5.4 if this could be a relevant information. There was a bug that was fixed in May 2011 wherein 4.5.4 reported too few hydrogen bonds. commit 91a481fad7ef0d87a4f8b2cb633c9dc40644350c Author: Erik Marklund er...@anfinsen.bmc.uu.se Date: Tue May 10 14:37:10 2011 +0200 Fixed long standing bug where the merging resulted in too few hbonds. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] strange protonate state
On 2012-11-19 09:57, Albert wrote: hello: I've got a K+ near an Asp residue. I found that If I include the K+ in H++ calculation, the Asp is deprotonated while it is protonated if I didn't include it. I am quite confused for this. I am just wondering will the g_protonate will solve this problem? thank you very much. best Albert This makes sense! The environment is made for a neutral group, which you get by either having a K+ or a proton near the Asp. Normal pdb2gmx will give you the correct topology. -- 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
Re: [gmx-users] strange protonate state
On 2012-11-19 10:42, Albert wrote: On 11/19/2012 10:27 AM, David van der Spoel wrote: On 2012-11-19 09:57, Albert wrote: hello: I've got a K+ near an Asp residue. I found that If I include the K+ in H++ calculation, the Asp is deprotonated while it is protonated if I didn't include it. I am quite confused for this. I am just wondering will the g_protonate will solve this problem? thank you very much. best Albert This makes sense! The environment is made for a neutral group, which you get by either having a K+ or a proton near the Asp. Normal pdb2gmx will give you the correct topology. hello David: thanks a lot for such kind reply and comments. Is there any paper concerning on this ion issue? The pdb2gmx make correct protonation state of residues in most case, however for some special case we probably need more solid evidence to be confirmed. Since the protonation state of residue have great impact on later MD productions. No paper, just basic biochemistry. In case you suspect an amino-acid should NOT have the default protonation you can run pdb2gmx interactively. This is however your responsibility as the algorithm is not perfect, in fact it only checks the protonation of histidine residues. thank you very much. best Albert -- 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
Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
1.076 15 N 1GLNNE2 15-1.0031 14.01 ; qtot 0.0732 16 H 1GLN HE21 16 0.4429 1.008 ; qtot 0.5161 17 H 1GLN HE22 17 0.4429 1.008 ; qtot 0.959 18 C 1GLN C 18 0.6123 12.01 ; qtot 1.571 19 O2 2GLNOC1 19-0.8055 16 ; qtot 0.8055 20 O2 2GLNOC2 20-0.8055 16 ; qtot 0 There is not such residue in rtp file (GLN with NH3+ and CO2- terminals) Please guide me how to resolve this problem and obtain correct topology file. This IS the correct topology file. Now you have to make a topology for your protein WITHOUT ligand and then merge it in a text editor, or better use an #include ligand.itp -- 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
Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
On 2012-11-17 15:37, Atila Petrosian wrote: Hi all. After using amber03 force field for protein-ligand simulation (pdb2gmx), I encountered with following error: Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus. Ligand in my system is a single residue (GLN). There are [GLN], [NGLN] and [CGLN] in rtp file of amber03 force field. Should this single residue be as both of [NGLN] and [CGLN]? How to fix this error? Any help will highly appreciated. Manually making a toplogy is your best best. Add an alanine after the gln then in the top file rename and remove atoms. GAFF is an alternative but it will not give you exactly the same charges and LJ parameters. -- 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
Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
On 2012-11-17 16:26, Atila Petrosian wrote: Dear David Thanks for your quick reply. You said Add an alanine after the gln then in the top file rename and remove atoms. I confused. Why ALA? ALA (alanine) is a residue which is very simple than GLN structurally. I should add alanine after the gln. But in which file? you make a separate molecule Gln-Ala using pymol or vmd and then run it through pdb2gmx, this will give you NGLN-CALA. Then you edit the top file (remove superfluous alanine atoms, rename the N in ALA to O2 etc) with a text editor until it is correct with help from the rtp file for CGLN. You may have to smooth the charges to keep it neutral. -- 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
Re: [gmx-users] g(r) does not go to 1 at long r -- bug in g_rdf?
On 2012-11-16 09:12, Pablo Englebienne wrote: Hi, I tried to calculate the radial distribution functions for a simple system: a 5nm a side cubic box with 10 Ne atoms and 10 Ar atoms, simulated for 100ns in NVT @ 300K. I was expecting to get an RDF with a peak, stabilizing to 1.0 at long distances. This was the case for the Ne-Ar RDF, but not for the Ne-Ne or Ar-Ar RDFs, which stabilize to about 0.9. I believe this is due to a problem in the normalization of the histograms with respect to the number of pairs available: there are N*N pairs for the Ne-Ar, while N*(N-1) for the Ne-Ne and Ar-Ar case. Did somebody else find an issue like this? I think that the issue may become not evident for a relatively large system, as N*N ~ N*(N-1) for large N. I put the relevant files if somebody wishes to reproduce it here: https://gist.github.com/4085292 I'll appreciate input on this and I can also file a bug if deemed necessary. Take care, Pablo Thanks for reporting. Can you please make a redmine issue of this and assign it to me? -- 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
Re: [gmx-users] Strange form of RDF curve
On 2012-11-15 18:53, shch406 wrote: Dear Gromacs users, I tried g_rdf function and have obtained a strange result: usually the RDF curve looks like relaxing oscillations around 1.0 constant level, but in my case it appears to be oscillation around exponent going from 0.0 at zero distance to 1.0 at large distances. Is the RDF obtained correct? I used the command as follows: g_rdf -f MT.trr -s MT.tpr -n rs.ndx -o MT.RD.xvg -bin 0.05 -pbc -rdf res_cog where file MT.trr contains ~150 ps of equilibrated trajectory of 582 residue protein in water; The reference group was chosen Water and the 1 group was taken from index file rs.ndx. The latter group contains two tip NHH groups of charged arginine. (This residue was inspected on exposing to solvent and showed one of the largest solvent accessible surface). Thanks in advance, Igor Shchechkin I think you need to switch the arguments, first side chain then water. -- View this message in context: http://gromacs.5086.n6.nabble.com/Strange-form-of-RDF-curve-tp5003001.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
Re: [gmx-users] Re:problem with simulation of freezing of water
On 2012-11-11 17:26, Justin Lemkul wrote: On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or by gromacs? In your opinion, if i want this structure of ice for my simulation, What can i do? Start by searching the literature for a suitable protocol. Ice simulations have been done before. As I said before, each water model has a different melting point, and hardly any of them correspond to the actual experimental value. See if you can produce a suitable simulation with a pressure of 1 bar (proof of concept) and then change conditions. What you have to keep in mind is that most water models were designed to work at ambient conditions for normal simulations. They do not necessarily work under extremes or produce useful results under those conditions. -Justin Try TIP4P/Ice -- 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
Re: [gmx-users] Polarisation model
On 2012-11-07 10:21, Volker Lesch wrote: Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one big problem namely polarisation. In AMBER I used the atomic point dipole model but this one is not implemented in Gromacs (please correct me if I am wrong). Are there any experienced data which compare the two models, atomic point dipole and shell?? Kind regards, Volker This is not implemented. The shell model works but with limited functionality, such that the Charmm model does not work completely. It would be interesting to have such a comparison although I expect few significant differences. -- 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
Re: [gmx-users] Polarisation model
On 2012-11-07 11:24, Volker Lesch wrote: On 11/07/2012 11:19 AM, David van der Spoel wrote: On 2012-11-07 10:21, Volker Lesch wrote: Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one big problem namely polarisation. In AMBER I used the atomic point dipole model but this one is not implemented in Gromacs (please correct me if I am wrong). Are there any experienced data which compare the two models, atomic point dipole and shell?? Kind regards, Volker This is not implemented. The shell model works but with limited functionality, such that the Charmm model does not work completely. It would be interesting to have such a comparison although I expect few significant differences. Hallo, thanks for this reply. So the shell model only works for simple systems like water. Is this correct? What are the exact limitations? Kind regards, Volker In Charmm there are additional terms for screening like the Thole potential, which is implemented in gmx but not really debugged thoroughly yet. However, the Charmm people also use some kind of non-bonded screening that is not implemented. -- 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
Re: [gmx-users] a question on g_hbond
On 2012-11-04 06:52, Acoot Brett wrote: Dear All, I have a protein complex PDB composed of chain A and Chain B. I want to dtermine the hydrogen bonds between chain A and chain B. By g_hbond it request me to input the group twice. But both chain A and chain B belong to group protein. In this situation how can I determine the hydrogen bond between chain A and B? you should make your own index file. e.g. using make_ndx. And if I want to which donor and acceptor form a hydrogen bond, which option of the g_hbond command has this function? I am looking forward to getting your reply. Cheers, Acoot -- 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
Re: [gmx-users] Cholesterol parameters (Charrm36) in GMX
On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- 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
Re: [gmx-users] Cholesterol parameters (Charrm36) in GMX
On 2012-11-01 09:47, Yorquant Wang wrote: Hi David: I have tested the script. The input are 1 charmm topology file, 2 corresponding charmm parameter file and 3 foldername. But there are a lots of top_all***.rtf files and par_all***.prm files in toppar_c36_aug12/toppar folder, I don't know which pair is the correct pair. Could you give me a clue? The new parameter for cholesterol is stored in chol_new.str. If it is OK that I just put chol_new.str into the toppar_c36_aug12/toppar/ folder and transfer it directly. Don't know. I think you need everything gromacs related that comes out. Do it in an empty directory. Thank you for replying! yorquant 2012/11/1 David van der Spoel sp...@xray.bmc.uu.se On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- 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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] Conceptual question about the representation of dihedral angles in Gromacs
On 2012-10-27 03:02, Andrew DeYoung wrote: Hi, If you have time, may I ask a conceptual question about how dihedral angles are specified in force fields? Consider ethane, a two-carbon hydrocarbon (H_3C-CH_3). It has two carbon atoms and six hydrogen atoms. Call the carbons C1 and C2. Hydrogens H1, H2, and H3 are bonded to C1. Hydrogens H4, H5, and H6 are bonded to C2. I would like to account for all possible H*-C1-C2-H* dihedral angles. From organic chemistry, I know that the rotational barrier of ethane is approximately 2.9 or 3 kcal/mol (see, for example, http://research.cm.utexas.edu/nbauld/teach/ethane.html). In the OPLS-AA force field, I have found parameters for the dihedral HC-CT-CT-HC: HC CT CT HC 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 ; hydrocarbon *new* 11/99 If I plot the potential energy V for these RB parameters on a plotter, it appears that the barrier height is about 0.9 kcal/mol (I converted from kJ/mol by dividing by 4.184). My question is, do the above parameters correspond to only a _single_ H-C-C-H dihedral (for example, H1-C1-C2-H4)? If so, then I will need to specify H1-C1-C2-H5 and H1-C1-C2-H6 in addition to H1-C1-C2-H4, I think. By doing so, I will be essentially adding 3 different plots: one for H1-C1-C2-H4, one for H1-C1-C2-H5 (phase-shifted by 120 degrees relative to H1-C1-C2-H4), and one for H1-C1-C2-H6 (phase-shifted by 240 degrees relative to H1-C1-C2-H4). In this way, the total barrier height will be 0.9 + 0.9 + 0.9 = 2.7 kcal/mol, approximately consistent with common knowledge from organic chemistry. Is this correct? In other words, the dihedral parameters represent a _single_ dihedral (for example, H1-C1-C2-H4), and _NOT_ a group of dihedrals (for example, H1-C1-C2-Hx where x = 4, 5, 6). Only by considering all possible dihedrals do we get the correct potential overall energy landscape. One conceptual problem I have with this, though, is that I get the 2.7 kcal/mol barrier height only by considering H1-C1-C2-Hx, where x = 4, 5, and 6. But I also will include H2-C1-C2-Hx and H3-C1-C2-Hx in my topology (where x = 4, 5, and 6 in each case). Does this mean that when I consider all possible dihedrals Hy-C1-C2-Hx (x = 4, 5, 6; y = 1, 2, 3), the overall barrier height will be 3 * 2.7 = 8.1 kcal/mol instead of 2.7 kcal/mol? All dihedrals are included in OPLS/AA, so you get 9 different ones, all in phase as well. On top of that is the Coulomb and Van der Waals interaction between the H, which will increase the barrier height (because the atoms are closest there). In other words the barrier is way too high. Thank you! Andrew -- 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
Re: [gmx-users] Dipole moment
On 2012-10-18 18:09, Nilesh Dhumal wrote: Hello, I am calculating the dipole moment auto-correlation function for my system which have 128 cation and 128 anion. I am saving the trajectory at each 2 ps and using this trajectory for further analysis. Can I save the dipole moment and three vectors at each 3 fs? The dipole moment of charged box is not defined, since if one ion hops over periodic boundary conditions to the next box the dipole makes an enormous jump. 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
Re: [gmx-users] The problem of converting CGenff parameters to those of Gromacs
On 2012-10-15 16:53, Peter C. Lai wrote: Isn't Mark's script outdated for this purpose? I just uploaded a new script that seems to work: http://www.gromacs.org/@api/deki/files/185/=charmm2gromacs-pvm.py Please check the comment on http://www.gromacs.org/Downloads/User_contributions/Other_software charmm forcefields specify epsilon and sigmas so you only need to convert them: gromacs(sigma) = (charmm(Rmin/2)/10) * (2/(2^(1/6))) gromacs(epsilon) = charmm(eps) * 4.184 For 1-4 pair interactions, gromacs(sigma1,4 i,j) = (charmm(Rmin/2_1,4_i) + charmm(Rmin/2_1,4_j))/(2^1/6) gromacs(eps1,4 i,j) = sqrt(charmm(eps_1,4_i) * charmm(eps_1,4_j)) * 4.184 On 2012-10-15 07:27:51AM -0700, spin wrote: Hello, everyone. I used the Mark's script's to convert the CGenff (version 2b7 ) parameter file to Gromacs .itp files. In the ffcharmmnb.itp, the script gave the c6 and c12, while the charmm's ffnonbond.itp showed epsilon and sigma.I do not understand the relation between the c6/c12 and epsilon and sigma, and I have a poor Perl skill. Can someone give me a solution? In addition, the script makes all atoms' charge zero in the file, which is not the case in the ffnonbond.itp. Why is it? Thank you! Qing Liu -- View this message in context: http://gromacs.5086.n6.nabble.com/The-problem-of-converting-CGenff-parameters-to-those-of-Gromacs-tp5002042.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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
Re: [gmx-users] Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)
On 2012-10-08 09:05, Emma Eriksson wrote: Thank you David for your response. Please see my reply below. On 2012-10-04 11:50, Emma Eriksson wrote: Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I run separate simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. The pull parameters are the following: pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DMPC pull_group1 = 2 pull_vec1 = 0 0 1 pull_init1 = x I have previously been using the same methodology in 4.0.5 without problems. When i run grompp in 4.5.5 I get the following error: Fatal error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310) The source of the first value, which should be the distance of pull group 1 is for me unknown. A value of ~4 is generated for all systems no matter what z distance is actually betwen the two groups (0-4 nm), so the value has no connection to the z distance between the groups. The second value is 0.5 times the x box length. I have read through pull.c, but I cannot find an explanation to why the x direction seems to be considered and not the z direction. When I run grompp with pull_geometry = distance or direction together with pull_dim = N N Y there is no problem. As I am not sure of the source of this error when running with cylinder I do not know if it is only related to the check or if the following simulation would be affected if I uncomment the check. Any suggestions to why this is happening and what I can do about it? Check the other pull_XXX values in mdout.mdp You have not specified all of them above, e.g. pull_direction? The pull parameter section in mdout.mdp are the following: ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = constraint ; Pull geometry: distance, direction, cylinder or position pull_geometry= cylinder ; Select components for the pull vector. default: Y Y Y pull_dim = Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1.0 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = no pull_nstxout = 10 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = DMPC pull_weights0= pull_pbcatom0= 0 pull_group1 = 2 pull_weights1= pull_pbcatom1= 0 pull_vec1= 0 0 1 pull_init1 = 0 pull_rate1 = 0 pull_k1 = 0 pull_kB1 = 0 I did not specify pull_dim as I understood it from the manual that this should not be used this for pull_geometry = cylinder (however, pull_dim will be set to the default Y Y Y in mdout.mdp). I specify pull_vec1 = 0 0 1, which should give the pull direction (z in this case). Did I misunderstand this somehow? When I specify pull_dim = N N Y I do not get any error with grompp, but instead I obtain the following: Pull group natoms pbc atom distance at start reference at t=0 0 5888 2944 149 20922 3.685 0 The distance between the two groups should be 0 but the program interpret is as 3.685, which is a value that I do not know where it comes from. I do not know what other options I can try or what is wrong here. Do you have any suggestion what is going on? Thank you. Not sure. Try replacing the cylinder with direction or so. Emma Thanks! Best regards, Emma -- 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-- 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
Re: [gmx-users] average velocity
On 2012-10-09 13:09, Dr. Vitaly Chaban wrote: Dear All - Is there a handy utility, which would give me an average velocity of a given particle during the simulation? g_traj -ov followed by g_analyze Thank you! Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- 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
Re: [gmx-users] Polarisablity of water using Gromacs
On 2012-10-09 14:26, Deepak Ojha wrote: Dear Gmx_users, I want to calculate instantaneous polarizability of water using GROMACS.I found there exists a water model which polarisable in gromacs with the itp file sw.itp. Is it possible to get the above mentioned using the sw water model in gromacs.Are there any tools like g_hbond which may help me get the same. -- DeepaK Ojha School Of Chemistry Selfishness is not living as one wishes to live, it is asking others to live as one wishes to live The polarizability is input, the polarization is output. You may want to use slightly more modern models available from http://virtualchemistry.org. -- 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
Re: [gmx-users] About Lincs Algorithim for Cyclic Peptide
; Velocity generation is on gen_temp= 310 ; temperature for velocity generation gen_seed= -1; random seed ; COM motion removal ; These options remove COM motion of the system nstcomm = 10 comm-mode = Linear comm-grps = System Thanks In Advance -- 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
Re: [gmx-users] Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)
On 2012-10-04 11:50, Emma Eriksson wrote: Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I run separate simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. The pull parameters are the following: pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DMPC pull_group1 = 2 pull_vec1 = 0 0 1 pull_init1 = x I have previously been using the same methodology in 4.0.5 without problems. When i run grompp in 4.5.5 I get the following error: Fatal error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310) The source of the first value, which should be the distance of pull group 1 is for me unknown. A value of ~4 is generated for all systems no matter what z distance is actually betwen the two groups (0-4 nm), so the value has no connection to the z distance between the groups. The second value is 0.5 times the x box length. I have read through pull.c, but I cannot find an explanation to why the x direction seems to be considered and not the z direction. When I run grompp with pull_geometry = distance or direction together with pull_dim = N N Y there is no problem. As I am not sure of the source of this error when running with cylinder I do not know if it is only related to the check or if the following simulation would be affected if I uncomment the check. Any suggestions to why this is happening and what I can do about it? Check the other pull_XXX values in mdout.mdp You have not specified all of them above, e.g. pull_direction? Thanks! Best regards, Emma -- 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 -- 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] Fatal error: Atomtype F not found
On 2012-10-04 04:39, Nur Syafiqah Abdul Ghani wrote: Dear Users, Right now i already done for creating the a gro file from antechamber to gromacs format of my molecule which is hexafluoroisopropanol. But when i want to minimize it in vacuum it show atomtype F not found. Im using oplsaa force field and i already change the atom type according to the force field. Do not combine force fields. Use antechamber and the gromacs conversion script to make a gromacs topology from it (amb2gmx.pl, search on google), then use amber force field in combination with this if you want to dissolve biomolecules or something like that. More organic molecules topologies can be found at http://virtualchemistry.org -- 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
Re: [gmx-users] Experiences with Gromacs scaling on US supercomputer centers?
On 2012-09-26 16:24, Michael Shirts wrote: Hi all, I'd be interested to know about people's experiences with Gromacs on US national computing centers. Which machines have it set up to scale the best? We're putting in an XSEDE request soon, and I'm trying to figure out which resource to request. Our system is semi-coarse-grained, using reaction field electrostatics, so we don't have to worry about PME. Of course, couldn't hurt to know about PME scaling as well. I'm interesting scalings with 100K - 300K atoms. Of course, best performance will probably change with 4.6 because of all the setup tweaks, but let's start with 4.5 scaling info! I guess you're aware of Roland Schulz' paper on cellulose systems on Jaguar? Over 100 million particles on 100,000 cores. We have done virus particles (1.2 million particles) on 2000 Cray XE6 cores (in Sweden). You are probably aware that scaling is different for different systems, in particular if you don't have waters. Your systems are relatively small for the big US computers of course, but it is often allowed to do ensemble calculations. I would suggest you get a test account for scaling tests for your particular system. Best, Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- 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
Re: [gmx-users] Automatic calculations of forces in tabulated potentials?
On 2012-09-08 13:41, Wu Chaofu wrote: Dear gmxers, Can the forces F(r) be calculated automatically from the potentials E(r) so that they can be replaced initially by zeros in the tabulated potentials? Thank you for any reply. Yours sincerely, Chaofu Wu No. But xmgrace or something like that can do it easily. -- 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
Re: [gmx-users] Problem with OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi
On 2012-08-29 05:32, jesmin jahan wrote: Dear All, I have installed gromacs VERSION 4.6-dev-20120820-87e5bcf with -DGMX_MPI=ON . I am assuming as OPENMP is default, it will be automatically installed. My Compiler is /opt/apps/intel11_1/mvapich2/1.6/bin/mpicc Intel icc (ICC) 11.1 20101201 And I am using OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi -s imd.tpr I was hopping this will run 16 processes each with 12 threads. However, in the log file I saw something like this: R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp.16 10.0270.0 1.8 Comm. coord. 16 10.0020.0 0.1 Neighbor search 16 10.1130.1 7.7 Force 16 11.2360.883.4 Wait + Comm. F16 10.0150.0 1.0 Update16 10.0050.0 0.4 Comm. energies16 10.0080.0 0.5 Rest 16 0.0760.0 5.1 --- Total 16 1.4810.9 100.0 --- Its not clear whether each of the 16 nodes runs 12 threads internally or not. Check your mpirun syntax. It may only give 16 cores to mdrun. If anyone knows about this, please let me know. Thanks for help. Best Regards, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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
