Re: [gmx-users] g_rmsf -res = average over time for each residue?
Hi Lin, How many residues do you have and how many points do you get? (Only answer for yourself). We're no substitute for your brain, you know... Cheers, Tsjerk On Oct 25, 2010 7:47 AM, Chih-Ying Lin chihying2...@gmail.com wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg *-[no]res* bool no Calculate averages for each residue abcrmsf.xvg = average over time for each residue? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reg; MD of DCE part II
- Original Message - From: vinothkumar mohanakrishnan kmvin...@gmail.com Date: Monday, October 25, 2010 15:57 Subject: [gmx-users] Reg; MD of DCE part II To: Discussion list for GROMACS users gmx-users@gromacs.org Hi gromacians I performed md simulation of 108 dichloroethane molecules in isothermal-isobaric ensemble with the box size 3.002*2.17*2.17. after the simulation my box size has changed considerably from the initial size to 2.87882 2.08095 2.08095.why this happens? Probably because it was not equilibrated (yet). my second question is can i have a control over the box dimensions changes during md (i.e when the box dimensions changes during md i want to change it only on one axis(say x axis) and want to keep the length of the other two axis (say y and z) same as that of my initial box size? any help is highly apprecited. Probably you can do what you want. See manual section 3.4.9 and 7.3.15. It's often a good place to search first ;-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reg; MD of DCE part II
Hi mark The system was well equiulibrated and the average temperature is 299.18 K and the pressure is 1.25 bar. I checked in the manual (gromacs version 4.0)l and there is no section like 3.4.9 and i as well checked 7.3.15. i too know that when there is no pressure coupling the box size wont change. what one will do if one wants to do in the NPT ensemble and wants to control the box dimensions? Regards Vinoth On Mon, Oct 25, 2010 at 12:15 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: vinothkumar mohanakrishnan kmvin...@gmail.com Date: Monday, October 25, 2010 15:57 Subject: [gmx-users] Reg; MD of DCE part II To: Discussion list for GROMACS users gmx-users@gromacs.org Hi gromacians I performed md simulation of 108 dichloroethane molecules in isothermal-isobaric ensemble with the box size 3.002*2.17*2.17. after the simulation my box size has changed considerably from the initial size to 2.87882 2.08095 2.08095.why this happens? Probably because it was not equilibrated (yet). my second question is can i have a control over the box dimensions changes during md (i.e when the box dimensions changes during md i want to change it only on one axis(say x axis) and want to keep the length of the other two axis (say y and z) same as that of my initial box size? any help is highly apprecited. Probably you can do what you want. See manual section 3.4.9 and 7.3.15. It's often a good place to search first ;-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reg; MD of DCE part II
- Original Message - From: vinothkumar mohanakrishnan kmvin...@gmail.com Date: Monday, October 25, 2010 18:10 Subject: Re: [gmx-users] Reg; MD of DCE part II To: Discussion list for GROMACS users gmx-users@gromacs.org Hi mark The system was well equiulibrated and the average temperature is 299.18 K and the pressure is 1.25 bar. ... and this means the system wants to contract (if this is an average pressure you've measured over a meaningful length of time). I checked in the manual (gromacs version 4.0)l and there is no section like 3.4.9 and i as well checked 7.3.15. OK, well look up in those chapters what GROMACS will do with pressure coupling (and plan to upgrade GROMACS). i too know that when there is no pressure coupling the box size wont change. what one will do if one wants to do in the NPT ensemble and wants to control the box dimensions? Given dimensions for a system at a given temperature are only compatible with a certain equilibrium pressure. PV=nRT and all that. You have to equilibrate to your reference pressure before you can expect the volume to stay within a small fluctuation of an average, and cannot choose P, V and T arbitrarily. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reg:Using Trjconv to combine two gro r pdb files
Hi gromacians I want to know how in the methanol-water tutorial ( http://manual.gromacs.org/current/online/mixed.html) they generated mixed.pdb or conf.gro (usr/local/gromacs/share/gromacs/tutor/mixed) using trjconv? any help is highly appreciated. Regards Vinoth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] solvation box type for nanotubes
Hello, Can we use rhombic dodecahedron solvation box for the PMF calculation on the small molecule diffusion into carbon nanotube. so that we can reduce 29% calculation time. If so then what could be the box size? Thank you. Regards, raj -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Reg:Using Trjconv to combine two gro r pdb files
- Original Message - From: vinothkumar mohanakrishnan kmvin...@gmail.com Date: Monday, October 25, 2010 19:31 Subject: [gmx-users] Reg:Using Trjconv to combine two gro r pdb files To: Discussion list for GROMACS users gmx-users@gromacs.org Hi gromacians I want to know how in the methanol-water tutorial (http://manual.gromacs.org/current/online/mixed.html) they generated mixed.pdb or conf.gro (usr/local/gromacs/share/gromacs/tutor/mixed) Maybe by concatenating two suitable single-solvent boxes. Or, you could start with a box of methol, increase its dimensions with a text editor, and then genbox to insert water solvent. Mark using trjconv? any help is highly appreciated. Regards Vinoth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Free energy calculations - desolvation energy of Na+
Hello all, I am trying calculate desolvation free energy of Na+ in water using option couple-moltype, not by creating B-topology in the .top file. At first, I switched off coulombic interaction using: couple-moltype = Na+ couple-lambda0 = vdw-q couple-lambda1 = vdw Then I tried to switch off LJ interaction using couple-lambda0 = vdw and couple-lambda1 = none, but obtained this warning: WARNING 1 [file equil_NVT000.mdp, line 95]: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used This is strange, because my .mdp file has only 94 lines. Thanks in advance for any help or suggestion. Best, Eva For convenience, I am pasting weak coupling algorithm section and free energy section from my .mdp file. The simulation was performed at constant volume using strong temperature coupling, since it was an equilibration run. ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = v-rescale tc-grps = system tau_t= 0.1 ref_t= 300 nsttcouple = 1 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.1 sc-alpha = 0.7 sc-power = 1 sc-sigma = 0.3 nstdhdl = 10 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 couple-moltype = Na+ couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] problem with g_density
Hi all, I have some difficulties with understanding the output of g_density command. I have a system composed of two Lennard Jones particles, A and B in a 20.712x20.712x20.712 simulation box. The parameters between the two particles are given such that they do not mix, but they undergo a phase separation. I want to investigate the density profile of the system, and I used the following command line to do that: g_density -f traj.xtc -n index.ndx -dens number -sl 100 The density profile for the two types of particles looks OK except the boundaries of the simulation box. I mean I would not expect to get a number other than 0 at the lower and upper boundaries. I have also searched the mailing list. There was an e-mail similar to that one, but it was not replied. I have attached the density profile in the attachment. Why is it the case? Regards -- Ozge Engin dens.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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 calculations - desolvation energy of Na+
eva.pluhar...@marge.uochb.cas.cz wrote: Hello all, I am trying calculate desolvation free energy of Na+ in water using option couple-moltype, not by creating B-topology in the .top file. At first, I switched off coulombic interaction using: couple-moltype = Na+ couple-lambda0 = vdw-q couple-lambda1 = vdw Then I tried to switch off LJ interaction using couple-lambda0 = vdw and couple-lambda1 = none, but obtained this warning: WARNING 1 [file equil_NVT000.mdp, line 95]: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used This is strange, because my .mdp file has only 94 lines. Regardless of the line number, the error message is pretty explicit - you probably have integrator = md in your .mdp file when you should have integrator = sd. -Justin Thanks in advance for any help or suggestion. Best, Eva For convenience, I am pasting weak coupling algorithm section and free energy section from my .mdp file. The simulation was performed at constant volume using strong temperature coupling, since it was an equilibration run. ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = v-rescale tc-grps = system tau_t= 0.1 ref_t= 300 nsttcouple = 1 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.1 sc-alpha = 0.7 sc-power = 1 sc-sigma = 0.3 nstdhdl = 10 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 couple-moltype = Na+ couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] COM pulling - speptide
C Johnson wrote: If you're proceeding blindly, then you're likely going to frustrate yourself to no end. There is literature relevant to what you're doing - pulling on peptides/proteins to unfold them is something that's been done. So you should have some methodological precedent. Non-Protein is a default group that should have been written to the .ndx file by make_ndx. The only reason I can see for this error to come up is if you've removed it from the pull.ndx file. If you're using my .mdp file, then Non-Protein is a temperature coupling group. -Justin I know there is literature relevant but is there any that explains how to do it in Gromacs? I don't know. All I implied was that some of the mystery can be taken out of the process. A good Methods section can be translated to the parameters needed by Gromacs as input. Usually how-to material is reserved for tutorials, not the literature. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with g_density
Ozge Engin wrote: Hi all, I have some difficulties with understanding the output of g_density command. I have a system composed of two Lennard Jones particles, A and B in a 20.712x20.712x20.712 simulation box. The parameters between the two particles are given such that they do not mix, but they undergo a phase separation. I want to investigate the density profile of the system, and I used the following command line to do that: g_density -f traj.xtc -n index.ndx -dens number -sl 100 The density profile for the two types of particles looks OK except the boundaries of the simulation box. I mean I would not expect to get a number other than 0 at the lower and upper boundaries. I have also searched the mailing list. There was an e-mail similar to that one, but it was not replied. I have attached the density profile in the attachment. Why is it the case? The behavior at the box boundaries is identical to that of the middle of the box (10 nm), which indicates to me that all interfaces are acting equivalently, which should be reassuring, I would think :) You're not seeing complete mixing of your two species, but there is some diffusion between the phases, otherwise both of your particles should drop to exactly zero density on either side of the box middle, wouldn't they? -Justin Regards -- Ozge Engin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with g_density
Hi, You're not seeing complete mixing of your two species, but there is some diffusion between the phases, otherwise both of your particles should drop to exactly zero density on either side of the box middle, wouldn't they? No, not if there are undulations of the interface. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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: 回复： [gmx-users] the first 10 mis sing interactions,except for exclusions...
英雄不再寂寞 wrote: Dear gmxers, The problem continues to puzzle me. I realize that only the EPON molecules with two phenyls lead to the problem. Then, may it be due to the ring catenations in the structure? Please give me some hints. Thanks a lot. Sounds like it could be a topology issue. Some tips are here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin Yours sincerely, Chaofu Wu, Dr. -- 原始邮件 -- *发件人:* Justin A. Lemkuljalem...@vt.edu; *发送时间:* 2010年10月24日(星期天) 上午8:20 *收件人:* Discussion list for GROMACS usersgmx-users@gromacs.org; *主题:* Re: [gmx-users] the first 10 missing interactions,except for exclusions... 英雄不再寂寞 wrote: Dear gmxers, I try to simulate a complex system using gmx-4.5.1. I have carried out the minimization without any errors, but when it comes to molecular dynamics, some errors are printed and given below. How to deal with this problem? Please give me some hints. Thanks a lot for any reply. Yours sincerely, Chaofu Wu, Dr. xiaowu...@linux-s38y:~/workshop mailto:xiaowu...@linux-s38y:~/workshop mdrun -s detamix_md01.tpr -o detamix_md01.trr -c detamix_md01.gro -e detamix_md01.edr -g detamix_md01.log -v -np 4 -N 4 :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.5.1 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, P盲r Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz, 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) 2001-2010, 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 General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: Option Filename Type Description .. Option Type Value Description -- .. Getting Loaded... Reading file detamix_md01.tpr, VERSION 4.5.1 (single precision) Starting 4 threads Loaded with Money NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off Making 1D domain decomposition 4 x 1 x 1 starting mdrun '40 deta + 100 epon862 + 1 SWCNT(10,10)' 400 steps, 4000.0 ps. step 0 NOTE: Turning on dynamic load balancing step 39500, will finish Mon Oct 25 02:51:47 2010vol 0.61 imb F 14% A list of missing interactions: Ryckaert-Bell. of 12880 missing 2 Molecule type 'EPON' the first 10 missing interactions, except for exclusions: Ryckaert-Bell. atoms 11 12 14 16 global 5481 5482 5484 5486 Ryckaert-Bell. atoms 16 21 23 11 global 5486 5491 5493 5481 --- Program mdrun, VERSION 4.5.1 Source code file: domdec_top.c, line: 356 Fatal error: 2 of the 79000 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.5 nm) or the two-body cut-off distance (1 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Jede der Scherben spiegelt das Licht (Wir sind Helden) xiaowu...@linux-s38y:~/workshop mailto:xiaowu...@linux-s38y:~/workshop Sounds like your system is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list.
[gmx-users] Re: COM pulling - speptide
If you're proceeding blindly, then you're likely going to frustrate yourself to no end. There is literature relevant to what you're doing - pulling on peptides/proteins to unfold them is something that's been done. So you should have some methodological precedent. Non-Protein is a default group that should have been written to the .ndx file by make_ndx. The only reason I can see for this error to come up is if you've removed it from the pull.ndx file. If you're using my .mdp file, then Non-Protein is a temperature coupling group. -Justin I know there is literature relevant but is there any that explains how to do it in Gromacs? Look into Justin's Umbrella Sampling tutorial. In step 5 it explain a COM pulling simulation. I use for this kind most of the time pull_geometry = position but then you must define a pulling direction (vector from 'pull_group0' to pull_group1'). For the 'pull_dim' i would set all 3 parameters to yes, if you want to do an afm-pulling experiment simulation. If you're pulling in the z-direction and have 'pull_dim = N N Y' your pull_group is free to move in the xy-plane (with no force acting on it), but if you think of an afm-experiment, there would also be a force-component in the x- and y-direction. Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] defining a 3 body user defined potential
Dear Amit As far as I know, 3-body interaction potential is not defined in gromacs. If you want to introduce it in Gromacs, you have to change the source code. It is not easy but not impossible and it was already done for TIP4P, see Kumar and Skinner, J. Phys. Chem. B, 112,8311-8318, 2008 I hope this help Ivan Amit Choubey wrote: Hi all, I was wondering if there is a way to define user defined potential which involves 3 particles. Thank you for any input. Amit -- --- Ivan Gladich, Ph.D. Dreyfus Postdoctoral Fellow Department of Chemistry Purdue University 560 Oval Drive, box 140 West Lafayette IN 47906 USA Room: 265C Tel:765-494-5225 e-mail: iglad...@purdue.edu web page: http://web.ics.purdue.edu/~igladich/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] trjconv t0/timestep parameter confusion
Hey Folks, I am having trouble with the t0 parameter in conjunction with -b. What I am trying to obtain is the following: Trajectory starts at 0 ends at 11. From this trajectory, I wanna write out frames from 1 to 11 (so discard the first 1) and set starting time to 0 so that I get a trajectory from 0 to 10. What I tried is the following: trjconv -f in.xtc -b 1 -t0 0 -o out.xtc This leads to a never ending trjconv process writing out a trajectory with frames and a deltat of 0. Did I misunderstood the parameters somehow? Tested with 4.0.7 and 4.5, time units are ps and trajectories have 1ps sampling. Best wishes Martin BTW: The workaround for this problem: First writing -b into a temp trajectory and then treating the tmp trajectory with -t0 0 -- Martin Hoefling Max Planck Institute for Biophysical Chemistry Theoretical Computational Biophysics Am Fassberg 11 37077 Goettingen Germany Phone: +49 551 201 2314 Fax: +49 551 201 2302 Mail: mhoe...@gwdg.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv t0/timestep parameter confusion
Maybe these parameters do not work in concert. Try a two-pass version - first discard the first 1, then later relabel the times. Mark - Original Message - From: Martin Hoefling mhoe...@gwdg.de Date: Tuesday, October 26, 2010 0:29 Subject: [gmx-users] trjconv t0/timestep parameter confusion To: gmx-users@gromacs.org Hey Folks, I am having trouble with the t0 parameter in conjunction with - b. What I am trying to obtain is the following: Trajectory starts at 0 ends at 11. From this trajectory, I wanna write out frames from 1 to 11 (so discard the first 1) and set starting time to 0 so that I get a trajectory from 0 to 10. What I tried is the following: trjconv -f in.xtc -b 1 -t0 0 - o out.xtc This leads to a never ending trjconv process writing out a trajectory with frames and a deltat of 0. Did I misunderstood the parameters somehow? Tested with 4.0.7 and 4.5, time units are ps and trajectories have 1ps sampling. Best wishes Martin BTW: The workaround for this problem: First writing -b into a temp trajectory and then treating the tmp trajectory with -t0 0 -- Martin Hoefling Max Planck Institute for Biophysical Chemistry Theoretical Computational Biophysics Am Fassberg 11 37077 Goettingen Germany Phone: +49 551 201 2314 Fax: +49 551 201 2302 Mail: mhoe...@gwdg.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 78, Issue 186
Hi Justin, thank you for suggestion about changing the integrator, but I would like to know why it is not possible to sample properly by md under these circumstances. 1. Do you know any papers about sampling efficiency of systems with almost or completely switched off particles? How does it depend on the kind of thermostat or barostat? 2. Note, that you can switch off the LJ particle also by creating B topology with sigma and epsilon equal to 0 in the .top file, not using couple-moltype. Doing so, there is no warning, but these approaches are equivalent. This seems like internal inconsistency in Gromacs. Thanks again for any hints. Best, Eva Hello all, I am trying calculate desolvation free energy of Na+ in water using option couple-moltype, not by creating B-topology in the .top file. At first, I switched off coulombic interaction using: couple-moltype = Na+ couple-lambda0 = vdw-q couple-lambda1 = vdw Then I tried to switch off LJ interaction using couple-lambda0 = vdw and couple-lambda1 = none, but obtained this warning: WARNING 1 [file equil_NVT000.mdp, line 95]: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used This is strange, because my .mdp file has only 94 lines. Regardless of the line number, the error message is pretty explicit - you probably have integrator = md in your .mdp file when you should have integrator = sd. -Justin Thanks in advance for any help or suggestion. Best, Eva For convenience, I am pasting weak coupling algorithm section and free energy section from my .mdp file. The simulation was performed at constant volume using strong temperature coupling, since it was an equilibration run. ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = v-rescale tc-grps = system tau_t= 0.1 ref_t= 300 nsttcouple = 1 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.1 sc-alpha = 0.7 sc-power = 1 sc-sigma = 0.3 nstdhdl = 10 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 couple-moltype = Na+ couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Free energy calculations - desolvation energy of Na+
eva.pluhar...@marge.uochb.cas.cz wrote: Hi Justin, thank you for suggestion about changing the integrator, but I would like to know why it is not possible to sample properly by md under these circumstances. 1. Do you know any papers about sampling efficiency of systems with almost or completely switched off particles? How does it depend on the kind of thermostat or barostat? I don't know about papers, but there are several relevant discussions in the list archive, i.e.: http://lists.gromacs.org/pipermail/gmx-users/2003-June/006054.html 2. Note, that you can switch off the LJ particle also by creating B topology with sigma and epsilon equal to 0 in the .top file, not using couple-moltype. Doing so, there is no warning, but these approaches are equivalent. This seems like internal inconsistency in Gromacs. Sorry, can't comment here. Topology manipulation is outdated as of version 4.0, but I guess it still works. Maybe some checks need to be implemented in this case. It certainly seems like there can be artifacts if other .mdp parameters are not set properly. -Justin Thanks again for any hints. Best, Eva Hello all, I am trying calculate desolvation free energy of Na+ in water using option couple-moltype, not by creating B-topology in the .top file. At first, I switched off coulombic interaction using: couple-moltype = Na+ couple-lambda0 = vdw-q couple-lambda1 = vdw Then I tried to switch off LJ interaction using couple-lambda0 = vdw and couple-lambda1 = none, but obtained this warning: WARNING 1 [file equil_NVT000.mdp, line 95]: For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used This is strange, because my .mdp file has only 94 lines. Regardless of the line number, the error message is pretty explicit - you probably have integrator = md in your .mdp file when you should have integrator = sd. -Justin Thanks in advance for any help or suggestion. Best, Eva For convenience, I am pasting weak coupling algorithm section and free energy section from my .mdp file. The simulation was performed at constant volume using strong temperature coupling, since it was an equilibration run. ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = v-rescale tc-grps = system tau_t= 0.1 ref_t= 300 nsttcouple = 1 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.1 sc-alpha = 0.7 sc-power = 1 sc-sigma = 0.3 nstdhdl = 10 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 couple-moltype = Na+ couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjconv t0/timestep parameter confusion
Hey Folks, I am having trouble with the t0 parameter in conjunction with -b. What I am trying to obtain is the following: Trajectory starts at 0 ends at 11. From this trajectory, I wanna write out frames from 1 to 11 (so discard the first 1) and set starting time to 0 so that I get a trajectory from 0 to 10. What I tried is the following: trjconv -f in.xtc -b 1 -t0 0 -o out.xtc This leads to a never ending trjconv process writing out a trajectory with frames and a deltat of 0. Did I misunderstood the parameters somehow? Tested with 4.0.7 and 4.5, time units are ps and trajectories have 1ps sampling. Best wishes Martin BTW: The workaround for this problem: First writing -b into a temp trajectory and then treating the tmp trajectory with -t0 0 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] problem with g_density
The problem is considerably worse than that. g_density is incorrect for every bin in the NPT ensemble. First, you have fluctuations in the z dimension. Second, g_density determines the bin as: slice = (int)(z / (*slWidth)); in calc_density() after wrapping coordinates around periodic z in all gromacs versions that I have seen, including v4.0.7 and v4.5.1. Thus, even the values near the bilayer center that appear to be ok are actually incorrect due to the addition of periodic-fluctuation-based noise. I've mentioned this on-list previously. Given this problem, the error introduced to g_hbond in the gmx4.5 series, and the lack of a proper test suite, I suggest always writing your own code that can test at least two frames of the output of any analysis program (even if your code only takes input as pdbs and runs slowly) so that you can develop some confidence in the output of the gromacs analysis tool. Chris. You're not seeing complete mixing of your two species, but there is some diffusion between the phases, otherwise both of your particles should drop to exactly zero density on either side of the box middle, wouldn't they? No, not if there are undulations of the interface. Cheers, Tsjerk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Job crash: checkpoint file
I am having exactly the same problem recently. The replica exchange job stops around 11000 steps. Switch to another cluster and the job is running fine. I wonder how often you've seen this type of crashing and any solutions for this? Thanks. Chuanyin Shi Department of Chemistry Biochemistry University of Oklahoma Email: c...@ou.edu From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 08, 2010 1:19 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Job crash: checkpoint file Jianhui Tian wrote: Dear GMX users, I am running a replica simulation and the job crashed with the following message: File input/output error: Cannot rename checkpoint file; maybe you are out of quota? From the mailling list, I see this might be a permission problem. However, I checked the file permission and nothing wrong was noticed. If I rerun the crashed simulation, it goes through the second time. This seems strong. Any suggestion is welcomed. I've seen this happen when our filesystem blips. It seems like you're able to run your job, so I don't think there's anything to do about it, except perhaps inquire with your sysadmins about the stability of the filesystem, and whether or not you can expect to have this happen frequently. -Justin JH -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Job crash: checkpoint file
On 2010-10-25 17.58, Shi, Chuanyin wrote: I am having exactly the same problem recently. The replica exchange job stops around 11000 steps. Switch to another cluster and the job is running fine. I wonder how often you've seen this type of crashing and any solutions for this? Thanks. Have you checked your quota? I had the same problem recently, and I was indeed out of quota. Chuanyin Shi Department of Chemistry Biochemistry University of Oklahoma Email: c...@ou.edu From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 08, 2010 1:19 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Job crash: checkpoint file Jianhui Tian wrote: Dear GMX users, I am running a replica simulation and the job crashed with the following message: File input/output error: Cannot rename checkpoint file; maybe you are out of quota? From the mailling list, I see this might be a permission problem. However, I checked the file permission and nothing wrong was noticed. If I rerun the crashed simulation, it goes through the second time. This seems strong. Any suggestion is welcomed. I've seen this happen when our filesystem blips. It seems like you're able to run your job, so I don't think there's anything to do about it, except perhaps inquire with your sysadmins about the stability of the filesystem, and whether or not you can expect to have this happen frequently. -Justin JH -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Job crash: checkpoint file
I wish the error would come from the quota. But the disk quota is fine, we still have 2.0TB on the scratch space which is shared by everyone. And I have other jobs running and no problem with writing outputs. I've tried smaller REMD jobs on the cluster using only 1 node (8 cpus) and seems to be no problem. But using 7 nodes and one (or two) node complains about that. And several weird files are generated: mdrun_mpi.80s-12939,v002.local.btr, mdrun_mpi.80s-12940,v002.local.btr, v002 is the name of the node. Chuanyin Shi Department of Chemistry Biochemistry University of Oklahoma Email: c...@ou.edu From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of David van der Spoel [sp...@xray.bmc.uu.se] Sent: Monday, October 25, 2010 11:21 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Job crash: checkpoint file On 2010-10-25 17.58, Shi, Chuanyin wrote: I am having exactly the same problem recently. The replica exchange job stops around 11000 steps. Switch to another cluster and the job is running fine. I wonder how often you've seen this type of crashing and any solutions for this? Thanks. Have you checked your quota? I had the same problem recently, and I was indeed out of quota. Chuanyin Shi Department of Chemistry Biochemistry University of Oklahoma Email: c...@ou.edu From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 08, 2010 1:19 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Job crash: checkpoint file Jianhui Tian wrote: Dear GMX users, I am running a replica simulation and the job crashed with the following message: File input/output error: Cannot rename checkpoint file; maybe you are out of quota? From the mailling list, I see this might be a permission problem. However, I checked the file permission and nothing wrong was noticed. If I rerun the crashed simulation, it goes through the second time. This seems strong. Any suggestion is welcomed. I've seen this happen when our filesystem blips. It seems like you're able to run your job, so I don't think there's anything to do about it, except perhaps inquire with your sysadmins about the stability of the filesystem, and whether or not you can expect to have this happen frequently. -Justin JH -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] defining a 3 body user defined potential
Thank you very much for the input Ivan. On Mon, Oct 25, 2010 at 5:46 AM, Ivan Gladich iglad...@purdue.edu wrote: Dear Amit As far as I know, 3-body interaction potential is not defined in gromacs. If you want to introduce it in Gromacs, you have to change the source code. It is not easy but not impossible and it was already done for TIP4P, see Kumar and Skinner, J. Phys. Chem. B, 112,8311-8318, 2008 I hope this help Ivan Amit Choubey wrote: Hi all, I was wondering if there is a way to define user defined potential which involves 3 particles. Thank you for any input. Amit -- --- Ivan Gladich, Ph.D. Dreyfus Postdoctoral Fellow Department of Chemistry Purdue University 560 Oval Drive, box 140 West Lafayette IN 47906 USA Room: 265C Tel:765-494-5225 e-mail: iglad...@purdue.edu web page: http://web.ics.purdue.edu/~igladich/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GPU slower than I7
Hi, My OS is Fedora 13 (64 bits) and I used gcc 4.4.4. I ran the program you sent me. Bellow are the results of 5 runs. As you can see the results are rougly the same [ren...@scrat ~]$ ./time 2.09 2.102991 [ren...@scrat ~]$ ./time 2.09 2.102808 [ren...@scrat ~]$ ./time 2.09 2.104577 [ren...@scrat ~]$ ./time 2.09 2.103943 [ren...@scrat ~]$ ./time 2.09 2.104471 Bellow are part of the /src/configure.h . . . /* Define to 1 if you have the MSVC _aligned_malloc() function. */ /* #undef HAVE__ALIGNED_MALLOC */ /* Define to 1 if you have the gettimeofday() function. */ #define HAVE_GETTIMEOFDAY /* Define to 1 if you have the cbrt() function. */ #define HAVE_CBRT . . . Is this OK? Renato 2010/10/22 Roland Schulz rol...@utk.edu: Hi, On Fri, Oct 22, 2010 at 3:20 PM, Renato Freitas renato...@gmail.com wrote: Do you think that the NODE and Real time difference could be attributed to some compilation problem in the mdrun-gpu. Despite I'm asking this I didn't get any error in the compilation. It is very odd that these are different for you system. What operating system and compiler do you use? Is HAVE_GETTIMEOFDAY set in src/config.h? I attached a small test program which uses the two different timers used for NODE and Real time. You can compile it with cc time.c -o time and run it with ./time. Do you get roughly the same time twice with the test program or do you see the same discrepancy as with GROMACS? Roland Thanks, Renato 2010/10/22 Szilárd Páll szilard.p...@cbr.su.se: Hi Renato, First of all, what you're seeing is pretty normal, especially that you have a CPU that is crossing the border of insane :) Why is it normal? The PME algorithms are just simply not very well not well suited for current GPU architectures. With an ill-suited algorithm you won't be able to see the speedups you can often see in other application areas - -even more so that you're comparing to Gromacs on a i7 980X. For more info + benchmarks see the Gromacs-GPU page: http://www.gromacs.org/gpu However, there is one strange thing you also pointed out. The fact that the NODE and Real time in your mdrun-gpu timing summary is not the same, but has 3x deviation is _very_ unusual. I've ran mdrun-gpu on quite a wide variety of hardware but I've never seen those two counter deviate. It might be an artifact from the cycle counters used internally that behave in an unusual way on your CPU. One other thing I should point out is that you would be better off using the standard mdrun which in 4.5 by default has thread-support and therefore will run on a single cpu/node without MPI! Cheers, -- Szilárd On Thu, Oct 21, 2010 at 9:18 PM, Renato Freitas renato...@gmail.com wrote: Hi gromacs users, I have installed the lastest version of gromacs (4.5.1) in an i7 980X (6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its mpi version. Also I compiled the GPU-accelerated version of gromacs. Then I did a 2 ns simulation using a small system (11042 atoms) to compare the performance of mdrun-gpu vs mdrun_mpi. The results that I got are bellow: My *.mdp is: constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2000 ps. nstlist = 10 ns_type = grid coulombtype = PME rvdw = 0.9 rlist = 0.9 rcoulomb = 0.9 fourierspacing = 0.10 pme_order = 4 ewald_rtol = 1e-5 vdwtype = cut-off pbc = xyz epsilon_rf = 0 comm_mode = linear nstxout = 1000 nstvout = 0 nstfout = 0 nstxtcout = 1000 nstlog = 1000 nstenergy = 1000 ; Berendsen temperature coupling is on in four groups tcoupl = berendsen tc-grps = system tau-t = 0.1 ref-t = 298 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 298 K. gen_vel = no RUNNING GROMACS ON GPU mdrun-gpu -s topol.tpr -v out Here is a part of the md.log: Started mdrun on node 0 Wed Oct 20 09:52:09 2010 . . . 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-Cycles Seconds % -- Write traj. 1 1021 106.075 31.7 0.2 Rest 1 64125.577 19178.6 99.8
Re: [gmx-users] (no subject)
I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log with -rerun grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log rm -f *#* I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total enregy vaies beteen +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectroy. Why the total energy is not contant. NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CT3 terminal
Hi, I use pdb2gmx command to convert a pdb file to a .gro and .top file(using CHARMM forcefield). For the C terminus, I use the CT3 option which is NCH3. When I use editconf to get a pdbfile from the .gro file generated, the C=0 and the NCH3 seem to clash in space in pymol. Is there a way of correcting this? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Gromos 45A4
Dear all, I have seen people using Gromos 45A4 force field to simulate sugars in Gromacs. But there is no such force field in the version 4.07 I'm using now. Where can I find the 45A4 force field? Or use some other force filed to replace it? sincerely, Liang-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res = does Gromacs do average over time for each residue ?
Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? = however, the results did not show difference with and without -res Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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_rmsf -res = does Gromacs do average over time for each residue ?
Chih-Ying Lin wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? The average is done over time and over the atoms in the residue. = however, the results did not show difference with and without -res I doubt that. Without -res, you get RMSF per atom. With -res, you get RMSF per residue. The output is inherently (and necessarily) different. -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res = what does this function work?
Hi From Manual http://manual.gromacs.org/current/online/g_rmsf.html g_rmsf = optiontypedefaultdescription -[no]res bool noCalculate averages for each residue what does this function work? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] (no subject)
I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log with -rerun grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total energy varies between +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectory. Why the total energy is not constant. NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_rmsf -res = what does this function work?
Chih-Ying Lin wrote: Hi From Manual http://manual.gromacs.org/current/online/g_rmsf.html g_rmsf = optiontypedefaultdescription -[no]res bool noCalculate averages for each residue what does this function work? Looking into the source code will answer this. -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res yes ? = should I type yes to activate the average-function ?
Hi g_rmsf -res yes ? g_rmsf -res no ? should I type yes to activate the average-function? As i tested g_rmsf -res, the average is not over time and not over the atoms in the residue. Anyway, how to activate the average function ? Thank you Lin Chih-Ying Lin wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? The average is done over time and over the atoms in the residue. = however, the results did not show difference with and without -res I doubt that. Without -res, you get RMSF per atom. With -res, you get RMSF per residue. The output is inherently (and necessarily) different. -Justin Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] Reg; MD of DCE part II
I performed md simulation of 108 dichloroethane molecules in isothermal-isobaric ensemble with the box size 3.002*2.17*2.17. after the simulation my box size has changed considerably from the initial size to 2.87882 2.08095 2.08095.why this happens? Density was obviously too lower under the conditions of the simulation. Look at the change of pressure, volume and density for the box during that simulation. my second question is can i have a control over the box dimensions changes during md (i.e when the box dimensions changes during md i want to change it only on one axis(say x axis) and want to keep the length of the other two axis (say y and z) same as that of my initial box size? any help is highly apprecited. Look at the pressure coupling settings, look at anisotropic pressure coupling. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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_rmsf -res yes ? = should I type yes to activate the average-function ?
Chih-Ying Lin wrote: Hi g_rmsf -res yes ? g_rmsf -res no ? should I type yes to activate the average-function? No. The command is either g_rmsf or g_rmsf -res. There is no yes or no required. As i tested g_rmsf -res, the average is not over time and not over the atoms in the residue. You will not get a plot over time. The calculation is done over time, but only the final result is plotted. If you have a plot of RMSF vs. residue, then averaging has been done over all the frames supplied, and over all the atoms in each residue. Unless you can prove that something has not been done correctly, then there is no need to repeatedly post the same question. -Justin Anyway, how to activate the average function ? Thank you Lin Chih-Ying Lin wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? The average is done over time and over the atoms in the residue. = however, the results did not show difference with and without -res I doubt that. Without -res, you get RMSF per atom. With -res, you get RMSF per residue. The output is inherently (and necessarily) different. -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] (no subject)
- Original Message - From: Nilesh Dhumal ndhu...@andrew.cmu.edu Date: Tuesday, October 26, 2010 10:50 Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS users gmx-users@gromacs.org I run a test simulation for -rerun. I didn't change the topology file. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb - p solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log with -rerun grompp -f md.mdp -c solvent-bmi-pf6-128.pdb - p solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun 3.trr -c solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log I calculate the total energy by g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg The total energy varies between +- 30.00 KJ/mol. It should be constant since I using same topology file and trajectory. Why the total energy is not constant. Those .tpr should be identical - but you can check that with gmxcheck. Reruns do neighbour-searching every step, whereas your normal simulation followed the nstlist setting. That's part of why my earlier advice suggested doing reruns for each simulation you wish to compare. You should be able to get good/better agreement for steps where nstlist directed neighbour-searching in the original run. Also, whether or not constraints have been applied (and when!) could influence the energies to about this degree. I don't recall the details here. Even once you've removed all algorithm-specific sources of difference, there are other sources of non-reproducibility, such as the assignment of particles to DD cells. Your original mdrun probably used dynamic load-balancing, and that cannot be reproduced in the DD used by the rerun. (Or indeed by a repeat of your original mdrun!) Setting -dlb no in the original simulation might be enough to get agreement here, or maybe mdrun -reprod will be required. Mark NIlesh On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate the energy at each step keeping the solvent configration same. IF I start a simulation with no charge on solute (case1), I have the energy for 1 step. I want to calculate the energy with charge on solute (case 2) with same configration water molecules. Each step I want to calculate the energy with and without charge on solute since the configration of solvent will be same for that step. I was thinking two make two topologies file with charge and with out charge on solute. I don't know how to use them simultaneously during the simulation. Well, you don't use them simultaneously. You run a simulation on whatever you think will generate a relevant conformational ensemble. Then you want to use mdrun -rerun twice on the resulting trajectory, using .tpr files based on .top files corresponding to the two cases in order to create your comparison. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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] CT3 terminal
- Original Message - From: Sai Pooja saipo...@gmail.com Date: Tuesday, October 26, 2010 7:26 Subject: [gmx-users] CT3 terminal To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, I use pdb2gmx command to convert a pdb file to a .gro and .top file(using CHARMM forcefield). For the C terminus, I use the CT3 option which is NCH3. When I use editconf to get a pdbfile from the .gro file generated, the C=0 and the NCH3 seem to clash in space in pymol. It looks like Par has borrowed the mechanism for generating two carboxylate oxygens on a C atom (one each cis and trans wrt the third generating atom) for generating one amide nitrogen, and the code doesn't check which of cis and trans is already occupied by the carboxyl oxygen. Please file a Bugzilla so that this gets fixed. A real solution requires some coding, but you can get a crude work-around by replacing 1 8 NT C CA N in share/top/charmm27.ff/aminoacids.c.tdb with 1 1 NT C CA O See chapter 5 for details. This NT will be too close to carboxyl C, and EM will be needed to fix things. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Total Energy of the system is positive?
Dear Gromacs users, I have simulated a system for 10ns and found out that the Total Energy of the system is positive and even the Epot of the system is positive. Is the data then reliable. Before I run the simulation i just check the energy min step and it was in fact negative. What does this mean? and There is no flactuations in temp and pressure. In solvent one it was negative and in solvent 2 it is negative. The same polymer but in diffrent solution. One solution give me positive TE and the other not. any explanation and also is my system normal. Best, Rob -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf = average over # of time frames ???
Hi
From source code = gmx_rmsf.c
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ,
deviation) of atomic positions ,
if (devfn) {
/* Calculate RMS Deviation */
for(i=0;(iisize);i++) {
aid = index[i];
for(d=0;(dDIM);d++) {
rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);
}
}
}
count += 1.0;
rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
Therefore, g_rmsf is the average of structure deviation over the time
frames.
However, I issued the commands ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 100 -s abc-crystal.tpr -o RMSF-abc-0th-100th.xvg
g_rmsf -f abc.xtc -b 100 -e 200 -s abc-crystal.tpr -o
RMSF-abc-100th-200th.xvg
g_rmsf -f abc.xtc -b 200 -e 300 -s abc-crystal.tpr -o
RMSF-abc-200th-300th.xvg
g_rmsf -f abc.xtc -b 300 -e 400 -s abc-crystal.tpr -o
RMSF-abc-300th-400th.xvg
g_rmsf -f abc.xtc -b 400 -e 500 -s abc-crystal.tpr -o
RMSF-abc-400th-500th.xvg
g_rmsf -f abc.xtc -b 500 -e 600 -s abc-crystal.tpr -o
RMSF-abc-500th-600th.xvg
g_rmsf -f abc.xtc -b 600 -e 700 -s abc-crystal.tpr -o
RMSF-abc-600th-700th.xvg
g_rmsf -f abc.xtc -b 700 -e 800 -s abc-crystal.tpr -o
RMSF-abc-700th-800th.xvg
g_rmsf -f abc.xtc -b 800 -e 900 -s abc-crystal.tpr -o
RMSF-abc-800th-900th.xvg
g_rmsf -f abc.xtc -b 900 -e 1000 -s abc-crystal.tpr -o
RMSF-abc-900th-1000th.xvg
Also, ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 1000 -s abc-crystal.tpr -o RMSF-abc-0th-1000th.xvg
Then I ploted,
RMSF-abc-0th-100th.xvg
RMSF-abc-100th-200th.xvg
RMSF-abc-200th-300th.xvg
RMSF-abc-300th-400th.xvg
RMSF-abc-400th-500th.xvg
RMSF-abc-500th-600th.xvg
RMSF-abc-600th-700th.xvg
RMSF-abc-700th-800th.xvg
RMSF-abc-800th-900th.xvg
RMSF-abc-900th-1000th.xvg
Also, I ploted
RMSF-abc-0th-1000th.xvg
The PLOT RMSF-abc-0th-1000th.xvg has all RMSF-Values much higher than those
from RMSF-abc-0th-100th.xvg / RMSF-abc-100th-200th.xvg
/ RMSF-abc-200th-300th.xvg / .. / RMSF-abc-900th-1000th.xvg...
It does not make sense... I supposed.
Did I misunderstand something ?
THank you
Lin
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[gmx-users] Re: CT3 terminal
Hello, I use pdb2gmx command to convert a pdb file to a .gro and .top file(using CHARMM forcefield). For the C terminus, I use the CT3 option which is NCH3. When I use editconf to get a pdbfile from the .gro file generated, the C=0 and the NCH3 seem to clash in space in pymol. Is there a way of correcting this? this sounds fishy, might be an error in the formation of the CT3. Have to look into that. What GROMACS version are you running? /Pär Bjelkmar-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
