[gmx-users] Charges in vacuum simulation
Hi all, I'm trying to run a vacuum simulation of my protein which has a non-zero charge. How to deal with this charge? Can I add counter ions in to my system? Would it be energetically stable? How can one bring a protein to its isoelectric point? -- 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] Testing the performance of
Thanks! Mark. I got solution to my problem. For my system, setting pinoffset = 0, 16 and pinstride = 1 for two simultaneous simulations gave much satisfactory performance both for Verlet and Group cutoff-scheme. I tried it for 4 simultaneous simulations also with pinoffset = 0, 8, 16, 24 and pinstride = 1 , and it works!! Command: mdrun -nt 16 -v -pin on -pinoffset 0 -pinstride 1 -deffnm file & mdrun -nt 16 -v -pin on -pinoffset 16 -pinstride 1 -deffnm file & Group: 21.559+21.879 = 43.348 ns/day Verlet: 20+20.293 = 40.293 ns/day Richa. -- 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] TRACE OF RMSD COMPARISON MATRIX
Thankyou!! sir. Your answer helped a lot. Richa On 2 July 2013 13:04, Tsjerk Wassenaar wrote: > Hi Richa, > > >From your explanation, I understand you want to know the sum of distances > between each frame and its corresponding filtered frame. I think it makes > more sense to sum squared distances, but that's a minor detail. > The (non-mass-weighted) RMSD between two structures, written as positional > vectors in 3N dimensional space, and properly rotated is: > > RMSD(a,b) = sqrt((a-b)'(a-b)) > > In your case, the objective is comparing a frame x and the frame filtered > by a set of eigenvectors, represented as the skinny matrix P: y = PP'x > > So, because the structures were fit prior to the covariance analysis > anyway, the MSD is > > MSD = (x-PP'x)'(x-PP'x) = x'x + x'PP'PP'x - 2x'PP'x > > Because the eigenvectors are an orthonormal set, P'P = I and we get > > MSD = x'x - x'PP'x > > Now, x'x is just the radius of gyration squared of the original structure, > so you can easily get that with g_gyrate for your trajectory. x'PP'x is the > inner product of the projections of x onto the eigenvectors in P, which you > get with g_anaeig -proj. So your objective is easily reached with some > relatively cheap calls to g_gyrate/g_anaeig and a bit of scripting in awk > or python, avoiding the determination of a whole RMSD matrix, just to get > the trace. In fact, it becomes rather trivial to do this for any subset of > eigenvectors you desire. > > As for the final answer, I would sum the MSD and take the square root, > rather than summing the square roots, to get a more meaningful answer. But > it's already unclear to me what these numbers would signify to begin with. > > Hope it helps, > > Tsjerk > > > > > On Tue, Jul 2, 2013 at 8:53 AM, Gaurav Goel wrote: > >> Following link might be helpful: >> http://orbeckst.github.io/GromacsWrapper/gromacs/core/fileformats/xpm.html >> >> -g >> -- >> Gaurav Goel >> Assistant Professor >> Department of Chemical Engineering >> Indian Institute of Technology, Delhi >> Hauz Khas, New Delhi 110016 >> India >> >> On 02-Jul-2013, at 10:45 AM, Richa Singh >> wrote: >> >> > Hello users, >> > >> > I'm using g_rms to compare my actual trajectory obtained from >> > simulation with the filtered trajectory (along given set of >> > eigenvectors), this gives me an RMSD comparison matrix in xpm format >> > where the values of the plot are not clear. Is there any way which can >> > help me to get the values along the diagonal of the matrix? >> > the command that i followed is: >> > g_rms -s ref.tpr -f actual.xtc -f2 filtered.xtc -m rmsd.xpm >> > >> > I want to calculate the trace of the matrix basically. >> > >> > >> > Regards.. >> > -- >> > 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 >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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] Testing the performance of
Hello, I want some inputs on observed performance of protein-in-water simulations run on a single server with 2 Intel Xeon E5-2660 processors. Each processor has 8C/16T, so total 16C/32T. My system is composed of 1643 beta-microglobulin atoms and 24699 water atoms. I ran several 500ps simulations with either 1, 2, or 4 simultaneous simulations on one server. Performance using the verlet and group schemes are reported below: For Verlet: mdrun -ntomp N -deffnm file where N is the no. of threads for Single simulation, 32 ns/day (N= 32 threads) Two simultaneous simulations, 4 + 0.25 = 4.25ns/day ( with N= 16 threads each) Four simultaneous simulations, 3.36+0.11+0.11+0.10=3.68ns/day. (N=8 threads each) mdrun -nt N -deffnm file where N is the no. of threads this gave me different results! for Single simulation, 28 ns/day (N= 32 threads) Two simulations, 13.8+13.5=27.3 ns/day ( with N= 16 threads each) --- For Group: -ntomp option is not available with Group cutoff-scheme. mdrun -nt N -deffnm file where N is the no. of threads for Single simulation, 38.5ns/day (N= 32 threads) Two simulations, 22.1+22.1=44.2 ns/day ( with N= 16 threads each) Four simulations, 12+11.9+12.2+11.8=48 ns/day ( N=8 threads each). Also, using -nt gives a warning to use -pin on , pinoffset option but if I use this option I get reduction in the performance again! the commands that I followed are: For Group cutoff-scheme and two simultaneous simulations -- mdrun -nt 16 -pin on -pinoffset 0 -deffnm file mdrun -nt 16 -pin on -pinoffset 8 -deffnm file the performance was 13.063+12.250=25.313 ns/day It is not clear to me why the performance decreases drastically on running simultaneous simulations with the verlet scheme. What is the correct way to use'-pin' option when running simultaneous simulations on a single server with multiple processors? The .mdp file that i used is (for Group, 'cutoff-scheme' option was omitted): ; Run parameters integrator = md; leap-frog integrator nsteps = 25; 2 * 25 = 500 ps, 0.5 ns dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 2 ps nstvout = 100 ; save velocities every 2 ps nstxtcout = 100 ; xtc compressed trajectory output every 2 ps nstenergy = 100 ; save energies every 2 ps nstlog = 100 ; update log file every 2 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; CUTOFF SCHEME cutoff-scheme = Verlet Thanks for your time. -- 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] TRACE OF RMSD COMPARISON MATRIX
Hello users, I'm using g_rms to compare my actual trajectory obtained from simulation with the filtered trajectory (along given set of eigenvectors), this gives me an RMSD comparison matrix in xpm format where the values of the plot are not clear. Is there any way which can help me to get the values along the diagonal of the matrix? the command that i followed is: g_rms -s ref.tpr -f actual.xtc -f2 filtered.xtc -m rmsd.xpm I want to calculate the trace of the matrix basically. Regards.. -- 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
