Yes. Compressibility of 0 for X/Y dimensions would tend to result in a static (i.e., non-compressible!) box. Look for some papers on lipid simulations - excessively low area/headgroup is a common problem, and there are a variety of opinions on how to approach this.
----- Original Message ---- From: maite lopez cabezas <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sunday, November 25, 2007 12:02:22 AM Subject: Re: [gmx-users] area by lipid Thanks Alan I tried with traj too and it's the same result....somebody use g_energy or g_traj. The cuestion is having x and y. The problem is I want to simulated a peptide-membrane system and the area couldn't be constant cause the insertion of the peptide increases the bilayer area. I think that is the compressibility , i changed my parameters from compressibility = 0 4.5e-5 ref-p = 0 1.0 to compressibility =4.5e-5 4.5e-5 ref-p = 1.0 1.0 and the area changed from 0.645 to 0.62 and it isn't a good valor. Maite These the output traj -ob # g_traj_331 -ob box.xvg -f dppc128_3ns_ok.xtc -e 1000 -s 3.tpr -nice 0 # # g_traj_331 is part of G R O M A C S: # # Grunge ROck MAChoS # @ title "Box vector elements" @ xaxis label "Time (ps)" @ yaxis label "(nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "XX" @ s1 legend "YY" @ s2 legend "ZZ" @ s3 legend "YX" @ s4 legend "ZX" @ s5 legend "ZY" 0 6.3696 6.3998 6.68 0 0 0 1 6.3696 6.3998 6.64996 0 0 0 2 6.3696 6.3998 6.63114 0 0 0 3 6.3696 6.3998 6.60618 0 0 0 4 6.3696 6.3998 6.59534 0 0 0 5 6.3696 6.3998 6.5969 0 0 0 6 6.3696 6.3998 6.58594 0 0 0 7 6.3696 6.3998 6.57235 0 0 0 8 6.3696 6.3998 6.57301 0 0 0 9 6.3696 6.3998 6.55283 0 0 0 10 6.3696 6.3998 6.5441 0 0 0 11 6.3696 6.3998 6.52643 0 0 0 12 6.3696 6.3998 6.54106 0 0 0 13 6.3696 6.3998 6.53806 0 0 0 14 6.3696 6.3998 6.54126 0 0 0 15 6.3696 6.3998 6.53768 0 0 0 On Nov 24, 2007 6:00 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > I didn't think g_energy was useful for that - I've always used g_traj -ob to > get box dimensions. If noone has a better answer, you should probably just > try that and see if you get the same effect. > > > ----- Original Message ---- > From: maite lopez cabezas <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Saturday, November 24, 2007 10:01:24 PM > Subject: [gmx-users] area by lipid > > > Hi: > > I am working on membrane simulation under lipid (DPPC, from Peter > Tieleman group site). I equilibrated dppc membrane for 10 ns and when > i got the area by lipid (x*y/ # lipids) using g_energy, i obtained > that the area is constant (0.64), there isn't any fluctuaction during > 10 ns..althougth the volumen isn't constant. > What's wrong in this simulation? > Any help will be highly appreciated. Thanks > > Maite > > > These g_energy output: > ---------------------------------------------------------- > @ legend length 2 > @ s0 legend "Kinetic-En." > @ s1 legend "Total-Energy" > @ s2 legend "Temperature" > @ s3 legend "Pressure-(bar)" > @ s4 legend "Box-X" > @ s5 legend "Box-Y" > @ s6 legend "Box-Z" > @ s7 legend "Volume" > @ s8 legend "Density-(SI)" > @ s9 legend "T-DPP" > @ s10 legend "T-SOL" > 0.000000 44884.128906 -299551.125000 309.756866 -2867.529297 > 6.369600 6.399800 6.680000 272.304596 974.509155 312.786591 > 307.970825 > 20.000000 44859.781250 -252572.656250 309.588837 62.661823 > 6.369600 6.399800 6.516144 265.625153 999.014282 310.579834 > 309.004639 > 40.000000 44840.101562 -252600.875000 309.453064 -93.168358 > 6.369600 6.399800 6.494525 264.743896 1002.339722 306.650665 > 311.105103 > 60.000004 45093.398438 -253077.312500 311.201111 -99.019768 > 6.369600 6.399800 6.491228 264.609497 1002.848877 310.111328 > 311.843567 > 80.000000 45020.613281 -252663.734375 310.698822 19.632711 > 6.369600 6.399800 6.504295 265.142151 1000.834167 309.710663 > 311.281342 > 100.000008 44901.433594 -252496.687500 309.876312 122.716400 > 6.369600 6.399800 6.506715 265.240784 1000.461975 312.459656 > 308.353394 > 120.000008 44964.890625 -252896.796875 310.314270 -124.685959 > 6.369600 6.399800 6.514557 265.560486 999.257568 306.510254 > 312.556793 > 140.000000 45168.968750 -252813.281250 311.722626 -290.249481 > 6.369600 6.399800 6.488441 264.495850 1003.279724 312.059570 > 311.524017 > 160.000000 44465.328125 -253265.328125 306.866638 368.317017 > 6.369600 6.399800 6.500315 264.979919 1001.446960 307.570343 > 306.451813 > 180.000015 44680.867188 -252064.906250 308.354126 -243.635345 > 6.369600 6.399800 6.491784 264.632141 1002.763062 309.213043 > 307.847809 > 200.000015 44827.578125 -252667.828125 309.366638 -166.550201 > 6.369600 6.399800 6.477999 264.070221 1004.896851 308.571106 > 309.835602 > 220.000015 44968.542969 -253124.671875 310.339447 -171.839508 > 6.369600 6.399800 6.487612 264.462097 1003.407837 309.458679 > 310.858673 > 240.000015 44708.015625 -253120.671875 308.541504 203.768204 > 6.369600 6.399800 6.498459 264.904236 1001.733032 307.988251 > 308.867645 > 2.............. > > > --------------------------------------------------------------------------------------------- > These is my .mdp file > --------------------------------------------------------------------------------------------- > ; VARIOUS PREPROCESSING OPTIONS > title = DM com Restricoes > cpp = /lib/cpp > include = > define = > > ; RUN CONTROL PARAMETERS > integrator = md > ; Start time and timestep in ps > tinit = 0 > dt = 0.002 > nsteps = 1500000 ; = 3000.0 ps > ; For exact run continuation or redoing part of a run > init_step = 0 > ; mode for center of mass motion removal > comm-mode = Linear > ; number of steps for center of mass motion removal > nstcomm = 1 > ; group(s) for center of mass motion removal > comm-grps = > > ; LANGEVIN DYNAMICS OPTIONS > ; Temperature, friction coefficient (amu/ps) and random seed > bd-temp = 300 > bd-fric = 0 > ld-seed = 1993 > > ; ENERGY MINIMIZATION OPTIONS > ; Force tolerance and initial step-size > emtol = 1000 > emstep = 0.01 > ; Max number of iterations in relax_shells > niter = 20 > ; Step size (1/ps^2) for minimization of flexible constraints > fcstep = 0 > ; Frequency of steepest descents steps when doing CG > nstcgsteep = 1000 > nbfgscorr = 10 > > ; OUTPUT CONTROL OPTIONS > ; Output frequency for coords (x), velocities (v) and forces (f) > nstxout = 50000 > nstvout = 50000 > nstfout = 50000 > ; Checkpointing helps you continue after crashes > nstcheckpoint = 1000 > ; Output frequency for energies to log file and energy file > nstlog = 1000 > nstenergy = 10 > ; Output frequency and precision for xtc file > nstxtcout = 500 > 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 = DPP SOL > > ; NEIGHBORSEARCHING PARAMETERS > ; nblist update frequency > nstlist = 5 > ; ns algorithm (simple or grid) > ns_type = grid > ; Periodic boundary conditions: xyz (default), no (vacuum) > ; or full (infinite systems only) > pbc = xyz > ; nblist cut-off > rlist = 1 > domain-decomposition = no > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = PME > rcoulomb-switch = 0 > rcoulomb = 1.0 > ; Dielectric constant (DC) for cut-off or DC of reaction field > epsilon-r = 1 > ; Method for doing Van der Waals > vdw-type = Cut-off > ; cut-off lengths > rvdw-switch = 0 > rvdw = 1.4 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = No > ; Extension of the potential lookup tables beyond the cut-off > table-extension = 1 > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = yes > > ; GENERALIZED BORN ELECTROSTATICS > ; Algorithm for calculating Born radii > gb_algorithm = Still > ; Frequency of calculating the Born radii inside rlist > nstgbradii = 1 > ; Cutoff for Born radii calculation; the contribution from atoms > ; between rlist and rgbradii is updated every nstlist steps > rgbradii = 2 > ; Salt concentration in M for Generalized Born models > gb_saltconc = 0 > > ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) > implicit_solvent = No > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > Tcoupl = berendsen > ; Groups to couple separately > tc-grps = DPP SOL > ; Time constant (ps) and reference temperature (K) > tau-t = 0.1 0.1 > ref-t = 310 310 > ; Pressure coupling > Pcoupl = berendsen > Pcoupltype = semiisotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau-p = 0.5 0.5 > compressibility = 0 4.5e-5 > ref-p = 0 1.0 > ; Random seed for Andersen thermostat > andersen_seed = 815131 > > ; SIMULATED ANNEALING > ; Type of annealing for each temperature group (no/single/periodic) > annealing = > ; Number of time points to use for specifying annealing in each group > annealing_npoints = > ; List of times at the annealing points for each group > annealing_time = > ; Temp. at each annealing point, for each group. > annealing_temp = > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = yes > gen-temp = 310.0 > gen-seed = 173529 > > ; OPTIONS FOR BONDS > constraints = all-bonds > ; Type of constraint algorithm > constraint-algorithm = Lincs > ; Do not constrain the start configuration > unconstrained-start = no > ; Use successive overrelaxation to reduce the number of shake > iterations > Shake-SOR = no > ; Relative tolerance of shake > shake-tol = 1e-04 > ; Highest order in the expansion of the constraint coupling matrix > lincs-order = 4 > ; Number of iterations in the final step of LINCS. 1 is fine for > ; normal simulations, but use 2 to conserve energy in NVE runs. > ; For energy minimization with constraints it should be 4 to 8. > lincs-iter = 1 > ; Lincs will write a warning to the stderr if in one step a bond > ; rotates over more degrees than > lincs-warnangle = 30 > ; Convert harmonic bonds to morse potentials > morse = no > > ; ENERGY GROUP EXCLUSIONS > ; Pairs of energy groups for which all non-bonded interactions are > excluded > energygrp_excl = > > ; NMR refinement stuff > ; Distance restraints type: No, Simple or Ensemble > disre = No > ; Force weighting of pairs in one distance restraint: Conservative or > Equal > disre-weighting = Conservative > ; Use sqrt of the time averaged times the instantaneous violation > disre-mixed = no > disre-fc = 1000 > disre-tau = 0 > ; Output frequency for pair distances to energy file > nstdisreout = 100 > ; Orientation restraints: No or Yes > orire = no > ; Orientation restraints force constant and tau for time averaging > orire-fc = 0 > orire-tau = 0 > orire-fitgrp = > ; Output frequency for trace(SD) to energy file > nstorireout = 100 > ; Dihedral angle restraints: No, Simple or Ensemble > dihre = No > dihre-fc = 1000 > dihre-tau = 0 > ; Output frequency for dihedral values to energy file > nstdihreout = 100 > > ; Free energy control stuff > free-energy = no > init-lambda = 0 > delta-lambda = 0 > sc-alpha = 0 > sc-sigma = 0.3 > ----------------------------------------------------------------------------------------------------- > _______________________________________________ > gmx-users mailing list 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] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > ____________________________________________________________________________________ > Be a better sports nut! Let your teams follow you > with Yahoo Mobile. Try it now. > http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ > _______________________________________________ > gmx-users mailing list 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] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list 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] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ____________________________________________________________________________________ Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ _______________________________________________ gmx-users mailing list 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] Can't post? Read http://www.gromacs.org/mailing_lists/users.php