RE: [gmx-users] Strange Gromacs4 trajectory visualisation with VMD
A quick and dirty fix that may save time is to view the trajectory in VMD with the DynamicsBonds drawing method instead of Lines (Graphics - Representation - Drawing Method - DynamicBonds). This make bond lines based on distance. Otherwise use the -pdb flag with whole or similar choice with trjconv. -Matt -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Kukol, Andreas Sent: Monday, December 07, 2009 3:48 AM To: Discussion list for GROMACS users Subject: [gmx-users] Strange Gromacs4 trajectory visualisation with VMD Hi all, When I look at the trajectory of a lipid/protein/water system generated with Gromacs 4.05 on four cores, the lipid bilayer looks messed up with bonds drawn all over the system, while the protein and water are displayed correctly. This is similar to previous Gromacs3 trajectories that had been shuffled, but not deshuffled before visualisation. Did anyone see similar problems and is there a solution to display the lipid correctly ? Many thanks Andreas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Msd of molecule center of mass (g_msd -mol with -rmcomm)
Hello, Does anyone have additional details about how the calculations are done for the -mol flag of g_msd when using -rmcomm? I am comparing results with and without the -mol flag. I presume that when -mol is used the file specified by the -o flag contains the average msd of the centers of mass of the molecules chosen with the index group and when -mol is not used, -o contains the average msd of atoms in the selected group. I have two specific questions: (1) Why would the msd of the COM of molecules be greater than the msd of the atoms at low dt (or at all length scales in some cases)? This does not happen when -rmcomm is not used but then the diffusion is wrong (too fast). (2) Why does the -mol msd curve up along a vertical asymtote at tmax when using -rmcomm? My system is a mixture of lipids in a bilayer run for 200 ns where COM of only the system was removed by mdrun. Trjconv was used to extract one leaflet of all lipids without water into an XTC file (e.g. upperleaflet-nojump.xtc). On this extracted sub-system, g_msd was run with -rmcomm and -lateral z while selecting for one lipid type with an index file. This was tried with and without -mol and comparing the outputs led to the questions above. Thanks, Matt --- Matthew I. Hoopes, Ph.D. Candidate Biophysics Graduate Group Department of Chemical Engineering and Material Science University of California, Davis 3118 Bainer Hall 1 Shields Ave. Davis, CA 95616 mihoo...@ucdavis.edu 530-752-6452 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] stochastic dynamics , langevin
Along these same lines... (a)is there an thermostat setting in GROMACS that comes close to the DPD thermostat as described in (T. Soddemann, B. D¨unweg, and K. Kremer. Dissipative particle dynamics: A useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. Phys. Rev. E, 68:046702, 2003.) (b) if nothing approaches DPD, how would a one go about starting to write a new thermostat in GROMACS? -Matt - Matthew Hoopes Biophysics Graduate Group University of California, Davis [EMAIL PROTECTED] 530-752-6452 - Hi, Brownina dynamics is a Langevin equation for the coordinates (no inertia). Stochastic dynamics is a Langevin equation for the velocities (with inertia). Everything depends on what you want to do, which you do not tell in detail. If you want to leave out the solvent, but you want to simulate a system in solvent, SD is not going to help you, since there is no implicit solvent potential, so your potential and therefore your sampling is nonsense. tau_t has no effect on the distribution, only on the dynamics. If you want the correct dynamics, you will have fit tau_t to reproduce some kinetic quantity that you are interested in. For different quantities tau_t can be different. Berk Date: Thu, 23 Oct 2008 15:31:16 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] stochastic dynamics , langevin Dear All, I am trying to perform Langevin dynamics of large peptides / proteins. After reading the manual going over some old mails in this list, I have two points I hope you could clear for me: [Gromacs version 3.3.3] 1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the proper keywords I should use for Langevin dynamics: integrator = sd ; bd-fric= 0 ; tau_t = 10 ; ref_t = 300 ; With bd-fric=0, the friction is taken as the inverse tau_t. 2) From your experience, what are good values of tau_t (or 1/tau_t) for simulating a protein? In 2006 list, David has commented that choosing tau_t is very important ( http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ). Your help is appreciated. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Smallest allowed cell size
Hi, I received the following error --- Program mdrun, VERSION 4.0 Source code file: domdec.c, line: 2933 Fatal error: Step 10: The X-size (-32.295326) times the triclinic skew factor (1.00) is smaller than the smallest allowed cell size (1.20) for domain decomposition grid cell 0 0 0 --- under the following conditions GROMACS 4.0 installed on a Cray XT4 at nics.utk.edu #PBS -l walltime=12:00:00,size=16 aprun -n 16 mdrun -maxh 29.5 The system has 84272 atoms in a box that is approx. 10x10x10. It works with 8 processors but I would think that this is fine divided up between 16 processors. Any suggestions for understanding this error message would be appreciated. Thanks, Matt - Matthew Hoopes Biophysics Graduate Group University of California, Davis [EMAIL PROTECTED] 530-752-6452 - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: implicit solvent in gromacs 4.0?
Depending on how you want to implement the solvent, you can do it now with tabulated potentials. I am moving a project I was doing in another MD package to GROMACS 4.0 that simulates CG lipid bilayers in an implicit solvent according to the following paper. I. R. Cooke and M. Deserno, Journal of Chemical Physics 123, 224710 (2005). -Matt - Matthew Hoopes Biophysics Graduate Group University of California, Davis [EMAIL PROTECTED] 530-752-6452 - jagannath mondal wrote: Hi, I was curious to know whether gromacs 4.0 supports implicit solvent simulation or not. If not, is there any possibility that the implicit solvent model will be implemented in near future ? No, 4.1 or 4.2. Thanks Jagannath Mondal Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Simulation of a protein confined in a box
As you may have seen in the GROMACS 4.0 manual, Walls can only be used with pbc=xy so its more of a floor/ceiling. You still may want a solution beyond the feature mentioned in chapter 7. Particle based realizations for walls may be a bit more work but very doable. See the following paper. Chenyue Xing and Roland Faller J. Phys. Chem. B, 112 (23), 7086-7094, 2008. -Matt -- Message: 3 Date: Sat, 11 Oct 2008 10:41:39 -0400 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Simulation of a protein confined in a box To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Lee Soin wrote: This seems to me a very complicated realization. Why doesn't GROMACS provide an easy way for wall simulation? How about reading manual section 7.3.20 Walls in the Gromacs-4.0 manual? I think that would be what you're after. -Justin 2008/10/11 Omer Markovitch [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Oh, I didn't read carefully. My suggestion would be, perhaps, to physically put atoms on the sides of the box (possibly, fill each side completely), and to place on them very high repulsion. You might want to freeze them up, and exclude their self interactions from the energy calculation. Good guess Suman. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Possibly what he is interested in is a system WITHOUT PBC? I don't think with PBC the system is really confined, since there is no true wall to reflect the colliding molecules. Thus to study the effect of real confinement, it is necessary to remove PBC and impose reflective boundary conditions. I am only guessing! :) --Suman. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sun Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
