[gmx-users] MSD and frequency of writing trajectories
Dear Gromacs Users, I have a question interpreting obtained msd data. I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules). During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very seldom (every 5 steps = 100 ps) but in xtc I have argon only (no water) and write more often (every 1000 steps = 2 ps). When I analysed the results using g_msd I was surprised that the msd curves obtained from trr and xtc trajectories differ a lot, what affect the resulting diffusion coefficients. If I save trr more often, like every 1 steps (20ps) the results from both files coincide. Does the msd results depend on how often you write trajectories? If yes, what frequency for writing the trajectories for future calculation of the diffusion coefficient would be reasonable and how long should be the calculations? Thanks you Anna --- Dr Anna Akinshina School of Chemical Engineering Analytical Science The University of Manchester, UK -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] MSD and frequency of writing trajectories
Hi, For particles that diffuse more than half a box length between frames will appear as if they haven't moved much, assuming you have periodic boundary conditions. Erik On 22 May 2013, at 11:41, Anna Akinshina anna.akinsh...@manchester.ac.uk wrote: Dear Gromacs Users, I have a question interpreting obtained msd data. I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules). During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very seldom (every 5 steps = 100 ps) but in xtc I have argon only (no water) and write more often (every 1000 steps = 2 ps). When I analysed the results using g_msd I was surprised that the msd curves obtained from trr and xtc trajectories differ a lot, what affect the resulting diffusion coefficients. If I save trr more often, like every 1 steps (20ps) the results from both files coincide. Does the msd results depend on how often you write trajectories? If yes, what frequency for writing the trajectories for future calculation of the diffusion coefficient would be reasonable and how long should be the calculations? Thanks you Anna --- Dr Anna Akinshina School of Chemical Engineering Analytical Science The University of Manchester, UK -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] MSD and frequency of writing trajectories
Sure. What's the MSD of a pendulum if you only sample at a rate equal to the period? How often you want to sample depends on the time scale of what you want to observe. That might be up to you to measure :-) Mark On Wed, May 22, 2013 at 11:41 AM, Anna Akinshina anna.akinsh...@manchester.ac.uk wrote: Dear Gromacs Users, I have a question interpreting obtained msd data. I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules). During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very seldom (every 5 steps = 100 ps) but in xtc I have argon only (no water) and write more often (every 1000 steps = 2 ps). When I analysed the results using g_msd I was surprised that the msd curves obtained from trr and xtc trajectories differ a lot, what affect the resulting diffusion coefficients. If I save trr more often, like every 1 steps (20ps) the results from both files coincide. Does the msd results depend on how often you write trajectories? If yes, what frequency for writing the trajectories for future calculation of the diffusion coefficient would be reasonable and how long should be the calculations? Thanks you Anna --- Dr Anna Akinshina School of Chemical Engineering Analytical Science The University of Manchester, UK -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] MSD normalization
Hi, I was just wondering how MSDs in Gromacs are normalized. I am calculatiing MSDs for my lipid system of different timesteps of simulation and I get much higher results for centre of mass calculations in comparison to mass-weighted one. And I thought about normalization issue, but I couldn't find any informations concerning that topic in manual. I'd be grateful if someone could explain how mean square displacement is normalized. Cheers, Slawomir-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MSD
Hi, I am working on the simulation of protein memberane. How can I calculate MSD (mean squar displacement) of bond lipid ( as those phosphate atomes are written 0.35 nm of protein)? I know that I must use g_msd for calculating, but I need “index file” that is included phosphate atoms within 0.35 nm of protein. how can I obtain this index file thanks in advance, Afsaneh Maleki -- 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] MSD
Quoting afsaneh maleki maleki.afsa...@gmail.com: Hi, I am working on the simulation of protein memberane. How can I calculate MSD (mean squar displacement) of bond lipid ( as those phosphate atomes are written 0.35 nm of protein)? I know that I must use g_msd for calculating, but I need index file that is included phosphate atoms within 0.35 nm of protein. how can I obtain this index file Please see g_dist -dist. -Justin thanks in advance, Afsaneh Maleki Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@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/search before posting! Please don't post (un)subscribe requests 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] msd
Hello together, i refer here to the problem with msd mentioned at the beginning of September (see also below): i calculate msd this time for monomers (not for molecules as before) and i still observe finite size effects for chains if they include fixed bonds ([constrains]), however this effect disappears when i replace fixed bonds by lj+fene bonds. Is it possible that lincs changes (slightly) the velocity field and hence the dynamics? Regards, Leonid Berk Hess wrote: Hi, g_msd calculates the msd for molecules, not for atoms. I guess that would explain the result when you half the chain length. It might also explain the box size effects, since whole chains will still have a reduction in MSD due to periodiciy with a box of 3 Rg. If you run g_msd without -mol you get the MSD per atom. Berk From: yel...@uni-mainz.de To: gmx-users@gromacs.org Date: Thu, 3 Sep 2009 15:22:40 +0200 Subject: [gmx-users] msd Hello together, i have a problem with msd. i simulate a melt of chain molecules consisting of 116 united atoms per chain. then i copy the box n times in x,y,z directions, repeat simulations and get a slightly different msd curves: in the time range between 1 ps and 10 ps it flattens out decreasing the curvature for larger boxes and at later time (10ps) follows at higher msd just parallel to the curve for smaller box. the boxe sizes were tried between 3 to 15 Rg's (gyration radii), so if it would be the finite size effect it should already disappear, but it doesnt. I also tried with different thermostats (sd, md with nose-hoover), different tau_t and also switching off the removal of com (then the box starts to fly after awhile) To check from the other side if it could be the finite size effect i reduce the length of the chains from 116 to 58 and the whole msd curve shifted up, also in ballistic regime where one can expect no influence of chain configuration. interesting that the shift is by factor of ~2 (although is not exactly): perhaps i'm just doing sth wrong! msd was calculated for chains using: g_msd -mol diff_mol.xvg is anybody aware of such things or has ideas what was done wrong? Thanks a lot in advance for any suggestions! Regards, Leonid ___ gmx-users mailing list gmx-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 Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ 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 not linear and c.o.m removal
Hi, I am running simulations of gaseous molecules (CH4, C2H6, CO2, N2) in a silica pore (4nm in diameter), cell dimensions, 46 x 44 x 37. This in an infinite pore in the z direction. I am interested in looking at diffusion but I am a bit concerned about the shape of my MSD curves, for a 5ns run, they start off fairly linear and then at around 2.5ns the slope stops being linear and levels out - in some cases the gradient goes to zero. So I am getting a curve rather than a straight line. This is the same whether or not I use the ?type z option in my command. At the moment I take the fit the curve between 0.5 - 2.5ns and ignore the second curvy half of the graph but I'd like to know why this is happening-Is it because the statistics become poorer for longer runs or is there something fundamentaly wrong with my system?. Does anyone know why this is happening? Another thing I am confused about is whether or not to remove the centre of mass when one is interested in obtaining the diffusion coefficient. I have seen on the gromacs forum that linear centre of mass removal is OK but a colleague has advised me not to remove it when studying diffusion. What about when applying an acceleration to obtain transport diffusion coefficients? Is c.o.m removal then needed or not? Currently, I am not using any centre of mass removal in my mdrun. Then I calculate the Ds to be g_msd ?mol -type z -f traj.xtc -s md.tpr -o msd_z.xvg D[ CO2] 140.5914 (+/- 75.9583) 1e-5 cm^2/s However when I include the ?rmcomm command when I run g_msd I get a very different Ds. g_msd -rmcomm -type z -mol -f traj.xtc -s md.tpr -o msd_z.xvg D[ CO2] 0.0118 (+/- 0.0364) 1e-5 cm^2/s It is difficult to say which value is correct as we don't have experimental data for comparison. Has anyone got any advice on this? I have pasted my typical input files below Much appreciated, C2H6.itp [ atomtypes ] ; typemasschargeptype c6c12 CH315.034 0.00 A0.35121.16236218 [ moleculetype ] ; name nrexcl ET 2 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 CH3 1 ET CH3 10.000 15.03452 2 CH3 1 ET CH3 10.000 15.03452 [ constraints ] ; ai aj funct c0 c1 1 2 1 0.2353 [ exclusions ] 1 2 2 1 .mdp ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = -I../top ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= none ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = yes ; nblist cut-off rlist= 1.5 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon-r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Shift ; cut-off lengths rvdw-switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables
[gmx-users] msd
Hello together, i have a problem with msd. i simulate a melt of chain molecules consisting of 116 united atoms per chain. then i copy the box n times in x,y,z directions, repeat simulations and get a slightly different msd curves: in the time range between 1 ps and 10 ps it flattens out decreasing the curvature for larger boxes and at later time (10ps) follows at higher msd just parallel to the curve for smaller box. the boxe sizes were tried between 3 to 15 Rg's (gyration radii), so if it would be the finite size effect it should already disappear, but it doesnt. I also tried with different thermostats (sd, md with nose-hoover), different tau_t and also switching off the removal of com (then the box starts to fly after awhile) To check from the other side if it could be the finite size effect i reduce the length of the chains from 116 to 58 and the whole msd curve shifted up, also in ballistic regime where one can expect no influence of chain configuration. interesting that the shift is by factor of ~2 (although is not exactly): perhaps i'm just doing sth wrong! msd was calculated for chains using: g_msd -mol diff_mol.xvg is anybody aware of such things or has ideas what was done wrong? Thanks a lot in advance for any suggestions! Regards, Leonid ___ 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] msd
Hi, g_msd calculates the msd for molecules, not for atoms. I guess that would explain the result when you half the chain length. It might also explain the box size effects, since whole chains will still have a reduction in MSD due to periodiciy with a box of 3 Rg. If you run g_msd without -mol you get the MSD per atom. Berk From: yel...@uni-mainz.de To: gmx-users@gromacs.org Date: Thu, 3 Sep 2009 15:22:40 +0200 Subject: [gmx-users] msd Hello together, i have a problem with msd. i simulate a melt of chain molecules consisting of 116 united atoms per chain. then i copy the box n times in x,y,z directions, repeat simulations and get a slightly different msd curves: in the time range between 1 ps and 10 ps it flattens out decreasing the curvature for larger boxes and at later time (10ps) follows at higher msd just parallel to the curve for smaller box. the boxe sizes were tried between 3 to 15 Rg's (gyration radii), so if it would be the finite size effect it should already disappear, but it doesnt. I also tried with different thermostats (sd, md with nose-hoover), different tau_t and also switching off the removal of com (then the box starts to fly after awhile) To check from the other side if it could be the finite size effect i reduce the length of the chains from 116 to 58 and the whole msd curve shifted up, also in ballistic regime where one can expect no influence of chain configuration. interesting that the shift is by factor of ~2 (although is not exactly): perhaps i'm just doing sth wrong! msd was calculated for chains using: g_msd -mol diff_mol.xvg is anybody aware of such things or has ideas what was done wrong? Thanks a lot in advance for any suggestions! Regards, Leonid ___ 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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 vs. time plot for molecules
Using g_msd on a group of atoms results in an msd vs. time plot which is the result of an average over all the atoms' motions. I would like to obtain the same plot, but for an average over the center of mass motions of a group of molecules. Using the -mol option results in a plot of the diffusion coefficient for each individual molecule. Do I need to use the -mw option for each molecule seperately and then average them together myself? Thank you for any ideas. --Mike Skaug ___ 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
Re: [gmx-users] msd and diffusion coefficient and getting unfolded trajectory
Hi, I did the calculation for water on both sides of bilayer. It is unlikely that water molecules donot cross the boundary. May be I need to wait for longer run such that molecules go out of box. I will check that. Thank you very much for your suggestions. Regards, Ananya. Ananya Debnath wrote: Hi, I want to calculate MSD (mean square displacement) for DPPC-WATER bilayer system, without using g_msd tool in gromacs, but using any other code, I need a trajcetory which is unfolded. From mails in mailing list I understand that people use trjconv -pbc nojump, to remove pbc. So I used pbc = xyz in .mdp file, and then trjconv -f traj.trr -s topol.tpr -o trajout.trr -pbc nojump Then if I calculate MSD (by my own code) from the trajout.trr , the result is same if I calculate from the original traj.trr file. Seeing the result I am confused, because -pbc nojump sholud stop the molecule from jumping across the box, then how can the MSD be same if it is with pbc? Maybe your trajectory does not have your relevant RMSD groups crossing the PBC, so trjconv is not doing anything relevant? Mark ___ 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] msd and diffusion coefficient and getting unfolded trajectory
Hi, I want to calculate MSD (mean square displacement) for DPPC-WATER bilayer system, without using g_msd tool in gromacs, but using any other code, I need a trajcetory which is unfolded. From mails in mailing list I understand that people use trjconv -pbc nojump, to remove pbc. So I used pbc = xyz in .mdp file, and then trjconv -f traj.trr -s topol.tpr -o trajout.trr -pbc nojump Then if I calculate MSD (by my own code) from the trajout.trr , the result is same if I calculate from the original traj.trr file. Seeing the result I am confused, because -pbc nojump sholud stop the molecule from jumping across the box, then how can the MSD be same if it is with pbc? If anyone writes me the proper way how to get unfolded trajectory, it will be a great help. Regards, Ananya. ___ 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
Re: [gmx-users] msd and diffusion coefficient and getting unfolded trajectory
Ananya Debnath wrote: Hi, I want to calculate MSD (mean square displacement) for DPPC-WATER bilayer system, without using g_msd tool in gromacs, but using any other code, I need a trajcetory which is unfolded. From mails in mailing list I understand that people use trjconv -pbc nojump, to remove pbc. So I used pbc = xyz in .mdp file, and then trjconv -f traj.trr -s topol.tpr -o trajout.trr -pbc nojump Then if I calculate MSD (by my own code) from the trajout.trr , the result is same if I calculate from the original traj.trr file. Seeing the result I am confused, because -pbc nojump sholud stop the molecule from jumping across the box, then how can the MSD be same if it is with pbc? Maybe your trajectory does not have your relevant RMSD groups crossing the PBC, so trjconv is not doing anything relevant? Mark ___ 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] MSD analysis
Dear all: I've got a DOPC/cholesterol system, and I want to get the MSD of the DOPCs near cholesterols. According to the literature, the overall movement of the each monolayer should be removed prior to the MSD analysis of individual molecules, my question is how should I do this? Thank you in advance. Jian ___ 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] MSD near specific molecules
Dear users: 1. I have a lipid bilayer of POPC with cholesterols. I'm trying to calculate the MSD of the POPCs which is nearest to cholesterols. The nearest POPCs are defined as those POPC whose C13 atoms to O6 atoms from cholesterol distances are less than a certain cutoff. Is there a good way to do that? 2. The overall lateral diffusion of each leaflet should be removed first. Using GMX3.3.2, I intend to get it by using trjconv -pbc nojump -center -boxcenter tric, is that right? 3. The two leaflets have been separated, and if I apply g_dist to the groups of upper-cholesterol and upper-POPC, and then use g_analyze -msd, I can only get the mutual diffusion of the center of mass of these two groups, is that right? Thank you. -DJ ___ 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
Re: [gmx-users] MSD
Roman Holomb wrote: Dear colleagues, Thanks for reply! Maybe I'm doing something wrong with using g_msd . no your system is freezing. I have computed MD (5ns) for system containing 100 anion and 100 cation molecules. Results of ACFs, RDFs look good but not MSD So I have 2_emi_BF4_100.tpr, 2_emi_BF4_100.trr, 2_indexEMI.ndx files. Index file contained numbers of EMI-cation molecules. Then I use command: g_msd -f 2_emi_BF4_100.trr -n 2_indexEMI.ndx -s 2_emi_BF4_100.tpr -o 2_emi_BF4_100_msd_EMI_full.xvg -mol 2_emi_BF4_100_msd_full_D_EMI.xvg And I have resulted Diffusion constants fitted from 0 to 5000 (ps) D[EMI]=(0.002+/-0.003)*10-5 cm2/s The resulted MSD graph is included. Then I try to use time 0-20 ps for fitting: g_msd -f 2_emi_BF4_100.trr -n 2_indexEMI.ndx -s 2_emi_BF4_100.tpr -beginfit 0 -endfit 20 -o 2_emi_BF4_100_msd_EMI_0_20.xvg -mol 2_emi_BF4_100_msd_0_20_D_EMI.xvg The resulted D: 0 to 20 (ps) D[EMI]=(0.508+/-0.253)*10-5 cm2/s. But MSD graphs look ideally the same. I'm not sure that program read number of molecules (instead of atoms). option -mol give only D for different molecules but not their average MSD Also -trestart option dosn't work and give me Segmentation Fault... Any comments are advisable. Thanks in advance! Sincerely /Roman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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, Assoc. Prof., Molecular Biophysics group, 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 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
Re: [gmx-users] MSD
Well. I think I agree with David 100 cations and 100 anions without solvent (am I correct?)... probably your system is freezing and an evidence of this is that the slope of your MSD graph tends to zero, so your D tends to zero too. But considering what you said about ACFs and RDFs, I think you know what you are doing and I´ll talk about only MSD. Your MSD plot is right for me. It starts with a non-linear part and after (near 1.5 ns) it become reasonable linear. But I think you need more statistic and I suggest you run more 5 ns of simulation the get a better linear part. The differences between values of D calculated with and without fitting is that in the first case you are fitting the Einstein equation (see manual) in hole graph. In the second case you are using times 0-20 and fitting the equation only in this part of the graph and, like you can see on it, the curve have a high slope in the beginning. Actually, you should use the begin-endfit option from 1.5 ns until the end of graph to fit the Einstein equation only to the linear part. About -trestart, it works restarting the initial position of the molecule every X ps. Try to use 1, 5 and 10 ps values for it and see what happen. Well... summarizing... try to run more 5 ns of simulation, run msd using -beginfit from the begin of linear part of your graph, play with t_restart values. I hope I helped you. Cheers Alexandre Suman de Araujo [EMAIL PROTECTED] UIN: 6194055 IFSC - USP - São Carlos - Brasil Roman Holomb wrote: Dear colleagues, Thanks for reply! Maybe I'm doing something wrong with using g_msd . I have computed MD (5ns) for system containing 100 anion and 100 cation molecules. Results of ACFs, RDFs look good but not MSD So I have 2_emi_BF4_100.tpr, 2_emi_BF4_100.trr, 2_indexEMI.ndx files. Index file contained numbers of EMI-cation molecules. Then I use command: g_msd -f 2_emi_BF4_100.trr -n 2_indexEMI.ndx -s 2_emi_BF4_100.tpr -o 2_emi_BF4_100_msd_EMI_full.xvg -mol 2_emi_BF4_100_msd_full_D_EMI.xvg And I have resulted Diffusion constants fitted from 0 to 5000 (ps) D[EMI]=(0.002+/-0.003)*10-5 cm2/s The resulted MSD graph is included. Then I try to use time 0-20 ps for fitting: g_msd -f 2_emi_BF4_100.trr -n 2_indexEMI.ndx -s 2_emi_BF4_100.tpr -beginfit 0 -endfit 20 -o 2_emi_BF4_100_msd_EMI_0_20.xvg -mol 2_emi_BF4_100_msd_0_20_D_EMI.xvg The resulted D: 0 to 20 (ps) D[EMI]=(0.508+/-0.253)*10-5 cm2/s. But MSD graphs look ideally the same. I'm not sure that program read number of molecules (instead of atoms). option -mol give only D for different molecules but not their average MSD Also -trestart option dosn't work and give me Segmentation Fault... Any comments are advisable. Thanks in advance! Sincerely /Roman ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
