[gmx-users] Protein is not at the centre of octahedron box
Dear All, I am doing a simulation for ligand-enzyme complex in a octahedron box. I have mentioned -c with editconf, but after energy minimization the protein is placed at the top of the box. Could you please suggest me how could I keep the protein at the centre of the octahedron box? Here are the details: After editconf> Volume =283.195nm^3 System size : 6.852 5.060 7.638 genbex> box_margin = 0.315 Removed 29370 atoms that were outside the box grompp> Using a fourier grid of 88x88x88, spacing 0.115 0.115 0.115 Thank You, Regards, Sukesh ___ 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
[gmx-users] RMS deviation after position restraint dynamics
Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although the deviation is very little). Could you please explain why is the deviation? Thank You, Regards, Sukesh ___ 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
[gmx-users] Problem with box-type after the extension of simulation
Dear All, I started a protein simulation for 100ps with octahedron box. After completion of that run I visualized the protein at the centre of the octahedron box by using trjconv. Then I have extended the simulation for another 500 ps by using tpbconv. But now it is showing as cubic box when I see the result after using trajconv (additionally some part of the protein is out of the box). I do not have any clue how the box type has been changed or where could I go wrong. Please comment. Thank you, Cheers, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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] Analysis of a simulation
Dear All, It is not clear from manual how to analyse my requirements after simulation. Could you please help me in the following regards: 1> How to get the graph on "occupancy of hydrogen bond interactions of ligands throughout 5 ns simulation" and "occupancy of a particular salt-bridge throughout the simulation" ? 2> I want to get a graph of the distances of some particular co-factor atoms and active site residues atoms throughout the simulation. Suppose I want the distance graph between DPM:C9B and Arg7:CA for total simulation. 3> Average hydrogen bond distance between active site residues and ligand. 4> RMSD of some particular residues from its initial structure. 5> Total formal charge residing at active site throughout the simulation (All +vely charge and -vely charge residues within 15 A radius of active site will be considered). It would be a great help if you could kindly give some sample commands for these analysis. Sorry for lots of questions. Thank You. Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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] Position restrained dynamics crash
Dear All, I am trying to do position restrained dynamics of a protein with co-factor in Gromacs Version 4. But after running for a while (1390 steps), the run is simply stopping. I am not getting any message on log file or terminal. Please help to identify the problem. This is my pr.mdp file parameters: ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 15000; total 30 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thank You, Regards, Sukesh. -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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] Dynamic cross correlation map
Dear All, Could you please tell how to plot the Dynamic Cross Correlation Matrix with Gromacs analysis tool or other tools. I want to know over a 20 ns simulation whether the motions of two residues or group of residues are correlated or anti correlated. For this I want to plot a dynamics cross correlation map in which I could get the precise information of group of atoms. I have done the following step and got the covariance matrix but don't know how to proceed further. >g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l covar.log -xpm covar.xpm -ascii covar.dat Waiting for your input. Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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] Dynamics cross correlation map
Dear All, Could you please tell how to get the Dynamic Cross Correlation map with Gromacs analysis tool or other tools. I want to know over a 20 ns simulation whether the motions of two residues or group of residues are correlated or anti correlated. For this I want to plot a dynamics cross correlation map in which I could get the precise information of group of atoms. I have done the following step and got the covariance matrix but don't know how to proceed further. >g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l covar.log -xpm covar.xpm -ascii covar.dat Waiting for your input. Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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] Dynamics cross correlation map
Hi Tsjerk, Thank you for your reply. May be I was not very clear with my previous post. I am not looking for covariance / atomic covariances map (ie., covar.xpm/covara.xpm) which are generated by g_covar tool in GROMACS. I am particularly trying to get correlation map (example: http://www.pnas.org/content/102/4/994/F2.large.jpg, http://www.pnas.org/content/99/26/16597/F3.small.gif). I hope there is a difference between covariance matrix and correlation matrix. The correlated motions between two atoms is calculated as the magnitude of the co-relation coefficient between the atoms. In case of a system it can be assessed by examining the magnitude of all pairwise cross-correlation coefficients. The cross-correlation coefficient, C(i,j) for each pair of atoms i and j is calculated as: C(i,j) = < delta r(i) * delta r(j) > / sqrt < sqr(delta r(i) ) > . sqrt < sqr(delta r(j) ) > , where delta r(i) is the displacement from mean position of the ith atom and < > symbol represents the time average. This function returns a matrix of all atom-wise cross-correlations whose elements, C(i,j), may be displayed in a graphical representation frequently termed a dynamical cross-correlation map, or DCCM. If C(i,j) = 1 the fluctuations of atoms i and j are completely correlated, if C(i,j) = -1 the fluctuations of atoms i and j are completely anticorrelated and if C(i,j) = 0 the fluctuations of i and j are not correlated. Now my query is there any tool like g_correlation (http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/GeneralizedCorrelations/index.html) by which I can get the cross-correlation matrix from covariance matrix or directly from trajectory file. Ref:1. Hünenberger PH, Mark AE, van Gunsteren WF; Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations; JMB 1995; 252:492-503 2. Oliver F. Lange, H. Grubmüller; Generalized Correlation for Biomolecular Dynamics; Proteins 2006; 62:1053-1061 Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- 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] Unstable model : need suggesstion
Dear All, I have done a simulation (in water) of PfPBGD model protein for 500 ps. But when I compared the secondary structure of my native protein structure vs structure after simulation. I observed that lot of unfolding is happening after simulation. So, my queries are: 1> Is there any way I can improve my model so that model protein become stable? 2> Is there any problem with my parameters which i have used for energy minimization, Position restrained dynamics and final simulation? 3> Can I improve my result changing the parameter files? what are the changes required? These are the parameters I have used for different run: em.mdp: cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002 ;ps nsteps = 400 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no pr.mdp: title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 1; total 20 ps. nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.4 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL CL- tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein SOL CL- ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 full.mdp: title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 25 ; total 500 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein SOL CL- tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein SOL CL- ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 I expect suggestion from expert. Thanks, Sukesh ___ 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
