Re: [gmx-users] umbrella sampling (PMF) position discrepancy
Hello Gromacs users, The solution that ended up working is selecting a different pull_pbcatom0 from the reference group, the protein, such that the atom is approx. in the center of mass of the protein. I hope that others may find this useful, Thanks to Martin Vesper and Justin Lemkul for their insights, Raphael On Tue, Sep 11, 2012 at 5:22 PM, Raphael Alhadeff < raphael.alhad...@mail.huji.ac.il> wrote: > Thank you all for your help, > > Sheeba- > Yes, I get both positive and negative results. I think what you describe > is what I would get if I used 'distance' for the geometry. > In any case, I have values from +2 to about -3, and they are not evenly > distributed (unlike the coordinates, which are more or less evenly > distributed) but are rather highly packed around -1 and then get > increasingly farther away from each other. > > Jianguo- > I did not see that thread before, I read it now but could not find > anything to solve my problem. > > Justin- > Thank you very much for your willingness to help, I will send the files > promptly. > > > Thanks again to everyone, I will post again should we find the problem and > solution for anyone who might find it useful.. > > Raphael > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] umbrella sampling (PMF) position discrepancy
Thank you all for your help, Sheeba- Yes, I get both positive and negative results. I think what you describe is what I would get if I used 'distance' for the geometry. In any case, I have values from +2 to about -3, and they are not evenly distributed (unlike the coordinates, which are more or less evenly distributed) but are rather highly packed around -1 and then get increasingly farther away from each other. Jianguo- I did not see that thread before, I read it now but could not find anything to solve my problem. Justin- Thank you very much for your willingness to help, I will send the files promptly. Thanks again to everyone, I will post again should we find the problem and solution for anyone who might find it useful.. Raphael -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] umbrella sampling (PMF) position discrepancy
Hi Justin, thank you for you quick reply. On Mon, Sep 10, 2012 at 6:41 PM, Justin Lemkul wrote: > > > On 9/10/12 11:22 AM, Raphael Alhadeff wrote: > >> Dear Gromacs users, >> >> I've been trying to run an umbrella sampling (for the purpose of pmf) >> using >> Gromacs 4.5.5. >> My system consists of a membrane protein transporter and a Na ion passing >> through it, from the water bulk on one side of the membrane to the water >> bulk on the other side. I've used the protein as the reference group and >> the Na ion as the pull group 1 (I've attached the mdp file below). I have >> used position geometry because to my understanding it is good for the case >> where the pulled group crosses the reference's COM. I made 31 frames where >> the ion is <0.2 nm apart, from -2 nm to +2 (in respect to the COM of the >> protein). I confirmed these distances using g_traj and g_dist on the >> starting gro files. >> >> As I run the g_wham analysis, using -v, I see that the 'position' of each >> of my frames are highly different than the distances I've measured in the >> gro files, not only in value but also relative to each other. The same >> numbers appear in the pull_x or pull_f (after converting appropriately) >> files. >> So what I don't understand is how does Gromacs calculate the values for >> pull_x (and thus for the 'position' for g_wham). I was under the >> impression >> it uses COM distance between group0 and group1, but trying to compare >> using >> g_traj or g_dist proved me wrong. >> I have pasted 5 datapoints as an example below, giving the distance >> measured by g_dist and the distance that pull_x gives: >> >> time(ps) g_dist(z)pull_x(1dz) >> 0 0.894-1.817 >> 10 0.857-1.698 >> 20 0.897-1.866 >> 30 0.890-1.913 >> 40 0.966-1.781 >> 50 0.819-1.76 >> >> >> I've read countless of threads before posting this, and could not find any >> answer, and will be very appreciative for some light into this. >> >> > The result of g_dist is the positive root of the distance equation. It > also uses x, y, and z components of the distance, while in your case only > the z component may be relevant. The dist.xvg file(s) will have each > component listed after the total distance in subsequent columns. > > I understand, and that is what I think I posted in the example. I have the z component of g_dist and following that my umbrella simulation pull_x 1dz value (which according to the parameters I gave in the mdp, should to the best of my knowledge, give the same number) yet the numbers are quite different. > >> I should mention that I am not using positional restraints on the protein. >> I assume that since the protein is inside the membrane and the ion is much >> smaller than the protein, the PR is not required, and I wanted the protein >> to be able to adjust slightly to the movement of the ion (this is a >> transporter, not a channel). >> If this is the reason that is causing me trouble I will be happy to have a >> short explanation on why this makes the distances seem somewhat random. >> >> Lastly, I will use this opportunity on the forum to have 2 technical >> clarifications - >> -Using pull_init = 0 (or any other number) does not overrun pull_start, >> rather it adds up, correct? >> > > Correct. The output of grompp prints the distances that will be used, as > a way to check. > > > -What is the difference between the profile.xvg created (default name) and >> the pmfintegrated.xvg that is sometimes being created, and how does g_wham >> decide whether to create one or not? >> >> > Which flag is giving you pmfintegrated.xvg? That's not a default name, so > without your g_wham command line, we can't guess. > > -Justin > > That is what I don't understand, I gave no flag for this file, my command line is simply g_wham -ix pull_x.dat -it tpr.dat -v Thank you again, Raphael > Thank you very much for the help.. >> >> Raphael >> >> mdp file: >> >> title = pmf >> >> integrator = md >> dt = 0.002 >> >> nsteps = 500; 10 ns >> nstcomm = 10 >> >> ; Output parameters >> nstxout = 5000 ; every 10 ps >> nstvout = 5000 >> nstxtcout = 5000 ; every 1 ps >> nstenergy = 5000 >> >> ; Bond parameters >> constraint_algorithm= lincs >> constrain
[gmx-users] umbrella sampling (PMF) position discrepancy
Dear Gromacs users, I've been trying to run an umbrella sampling (for the purpose of pmf) using Gromacs 4.5.5. My system consists of a membrane protein transporter and a Na ion passing through it, from the water bulk on one side of the membrane to the water bulk on the other side. I've used the protein as the reference group and the Na ion as the pull group 1 (I've attached the mdp file below). I have used position geometry because to my understanding it is good for the case where the pulled group crosses the reference's COM. I made 31 frames where the ion is <0.2 nm apart, from -2 nm to +2 (in respect to the COM of the protein). I confirmed these distances using g_traj and g_dist on the starting gro files. As I run the g_wham analysis, using -v, I see that the 'position' of each of my frames are highly different than the distances I've measured in the gro files, not only in value but also relative to each other. The same numbers appear in the pull_x or pull_f (after converting appropriately) files. So what I don't understand is how does Gromacs calculate the values for pull_x (and thus for the 'position' for g_wham). I was under the impression it uses COM distance between group0 and group1, but trying to compare using g_traj or g_dist proved me wrong. I have pasted 5 datapoints as an example below, giving the distance measured by g_dist and the distance that pull_x gives: time(ps) g_dist(z)pull_x(1dz) 0 0.894-1.817 10 0.857-1.698 20 0.897-1.866 30 0.890-1.913 40 0.966-1.781 50 0.819-1.76 I've read countless of threads before posting this, and could not find any answer, and will be very appreciative for some light into this. I should mention that I am not using positional restraints on the protein. I assume that since the protein is inside the membrane and the ion is much smaller than the protein, the PR is not required, and I wanted the protein to be able to adjust slightly to the movement of the ion (this is a transporter, not a channel). If this is the reason that is causing me trouble I will be happy to have a short explanation on why this makes the distances seem somewhat random. Lastly, I will use this opportunity on the forum to have 2 technical clarifications - -Using pull_init = 0 (or any other number) does not overrun pull_start, rather it adds up, correct? -What is the difference between the profile.xvg created (default name) and the pmfintegrated.xvg that is sometimes being created, and how does g_wham decide whether to create one or not? Thank you very much for the help.. Raphael mdp file: title = pmf integrator = md dt = 0.002 nsteps = 500; 10 ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstxtcout = 5000 ; every 1 ps nstenergy = 5000 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.16 pme_order = 4 ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein POP Sol_Ions tau_t = 0.5 0.5 0.5 ref_t = 310 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 2.0 compressibility = 4.5e-54.5e-5 ref_p = 1.0 1.0 ; Generate velocities is off gen_vel = yes gen_seed= -1 ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = position pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = Protein pull_group1 = r_4608 pull_init1 = 0 0 0 pull_vec1 = 0 0 1 pull_rate1 = 0.0 pull_k1 = 1000 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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_wham Error bars
Hello everyone, I wanted to ask if anyone knows how to compute standard deviation, for the sake of adding error bars to an energy profile output using g_wham (PMF using umbrella sampling in my case). Just to clarify, I am talking about the deviation of the energy profile on ONE simulation (composed of 25 "windows" in my case, with overlap but no repeats). Thanks in advance, Raphael ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
