Though I doubt it will make a difference, it may be useful to put a space between the values in
> ref_p= 1.01.0 ; reference pressure, x-y, z (in bar) > compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 > tau_t= 0.50.5;0.5 ; time constant, in ps but in any case, this could be poor pre-equilibration prior to dynamic simulations. Also, you have a relatively loose barostat in conjunction with a loose thermostat (0.5 ps), so the initial shockwaves linger in the system. Try the default constants of tau_p=2.0 and tau_t = 0.1. Nose-Hoover thermostat (algorithmically oscillatory) does not help with long ref_t either, maybe try v-rescale. Alex n> Dear all, n> I am new to lipid simulation. I have downloaded the pope.pdb, n> pope.itp, lipid.itp from Tieleman's web site n> (http://wcm.ucalgary.ca/tieleman/downloads). And I have made a n> directory named gromos53a6_lipid.ff followed Justin's n> tutorial n> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html). n> Then I use pope.pdp to run a pure 340 POPE lipid MD at 310K. But I n> find that the box of xy dimension will shrink from n> 9.6nm*9.5nm to 9.0nm*8.9nm after 20 ns, then it fluctuates at that n> value till 200ns. The box of z dimension will increase a little to n> hold the volume constant. This will lead to the area per lipid decreased from 0.54 nm^2 to n> 0.47nm^2. At the same time, I find the order parameter of lipid n> tail (Scd) is too big (above 0.3). Does any one know where the problem is? n> When I use dppc128.pdb from Tieleman's web site to run a pure n> DPPC lipid MDat 323K, the box will not shrink. And the area per n> lipid of DPPC is in accordance with literature, about 0.62nm^2. n> The water model is SPC. My mdp file is also from Justin's n> tutorial. Followed is my mdp file of POPE: n> title= KALP15-DPPC Production MD n> ; Run parameters n> integrator= md; leap-frog integrator n> nsteps= 100000000; 2 * 500000 = 1000 ps (1 ns) n> dt = 0.002; 2 fs n> ; Output control n> nstxout= 0; save coordinates every 2 ps n> nstvout= 0; save velocities every 2 ps n> nstxtcout= 1000; xtc compressed trajectory output every 2 ps n> nstenergy= 1000; save energies every 2 ps n> nstlog= 1000; update log file every 2 ps n> ; Bond parameters n> continuation= yes ; Restarting after NPT n> constraint_algorithm = lincs; holonomic constraints n> constraints= all-bonds ; all bonds (even heavy atom-H bonds) constrained n> lincs_iter= 1 ; accuracy of LINCS n> lincs_order= 4 ; also related to accuracy n> ; Neighborsearching n> ns_type= grid; search neighboring grid cels n> nstlist= 5 ; 10 fs n> rlist= 1.2; short-range neighborlist cutoff (in nm) n> rcoulomb= 1.2; short-range electrostatic cutoff (in nm) n> rvdw= 1.2; short-range van der Waals cutoff (in nm) n> ; Electrostatics n> coulombtype= PME; Particle Mesh Ewald for long-range electrostatics n> pme_order= 4 ; cubic interpolation n> fourierspacing= 0.16; grid spacing for FFT n> ; Temperature coupling is on n> tcoupl= Nose-Hoover ; More accurate thermostat n> tc-grps= POPE SOL;SOL_CL; three coupling groups - more accurate n> tau_t= 0.50.5;0.5 ; time constant, in ps n> ref_t= 310 310;323 ; reference temperature, one for each group, in K n> ; Pressure coupling is on n> pcoupl= Parrinello-Rahman ; Pressure coupling on in NPT n> pcoupltype= semiisotropic ; uniform scaling of x-y box vectors, independent z n> tau_p= 2.0 ; time constant, in ps n> ref_p= 1.01.0 ; reference pressure, x-y, z (in bar) n> compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 n> ; Periodic boundary conditions n> pbc = xyz; 3-D PBC n> ; Dispersion correction n> DispCorr= EnerPres; account for cut-off vdW scheme n> ; Velocity generation n> gen_vel= no; Velocity generation is off n> ; COM motion removal n> ; These options remove motion of the protein/bilayer relative to the solvent/ions n> nstcomm = 1 n> comm-mode = Linear n> comm-grps = POPE SOL n> ; Scale COM of reference coordinates (when postion restraint) n> ;refcoord_scaling = com n> And my topol file: n> #include "gromos53a6_lipid.ff/forcefield.itp" n> #include "pope.itp" n> ; Include water topology n> #include "gromos53a6_lipid.ff/spc.itp" n> ; System specifications n> [ system ] n> 340-Lipid POPE and CNP n> [ molecules ] n> ; molecule name nr. n> POPE 340 n> SOL 6729 n> Thanks in advance, n> Nie Xuechuan n> Shanghai Institute of Applied Physics, Chinese Academy of Sciences -- Best regards, Alex mailto:[email protected] -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
