On 4/11/15 8:25 AM, niexuechuan wrote:
Dear all, I am new to lipid simulation. I have downloaded the pope.pdb, pope.itp, lipid.itp from Tieleman's web site (http://wcm.ucalgary.ca/tieleman/downloads). And I have made a directory named gromos53a6_lipid.ff followed Justin's tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html). Then I use pope.pdp to run a pure 340 POPE lipid MD at 310K. But I find that the box of xy dimension will shrink from 9.6nm*9.5nm to 9.0nm*8.9nm after 20 ns, then it fluctuates at that value till 200ns. The box of z dimension will increase a little to hold the volume constant. This will lead to the area per lipid decreased from 0.54 nm^2 to 0.47nm^2. At the same time, I find the order parameter of lipid tail (Scd) is too big (above 0.3). Does any one know where the problem is?
This could very well be due to suboptimal parameters. Has anyone ever verified that these POPE parameters produce APL and order parameters in agreement with experimental values over such long time frames?
Lipid force fields are very sensitive and not all parameter sets are created equal. -Justin
When I use dppc128.pdb from Tieleman's web site to run a pure DPPC lipid MDat 323K, the box will not shrink. And the area per lipid of DPPC is in accordance with literature, about 0.62nm^2. The water model is SPC. My mdp file is also from Justin's tutorial. Followed is my mdp file of POPE: title= KALP15-DPPC Production MD ; Run parameters integrator= md; leap-frog integrator nsteps= 100000000; 2 * 500000 = 1000 ps (1 ns) dt = 0.002; 2 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; 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 cels nstlist= 5 ; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; 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= Nose-Hoover ; More accurate thermostat tc-grps= POPE SOL;SOL_CL; three coupling groups - more accurate tau_t= 0.50.5;0.5 ; time constant, in ps ref_t= 310 310;323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype= semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p= 2.0 ; time constant, in ps ref_p= 1.01.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, 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 ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = POPE SOL ; Scale COM of reference coordinates (when postion restraint) ;refcoord_scaling = com And my topol file: #include "gromos53a6_lipid.ff/forcefield.itp" #include "pope.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" ; System specifications [ system ] 340-Lipid POPE and CNP [ molecules ] ; molecule name nr. POPE 340 SOL 6729 Thanks in advance, Nie Xuechuan Shanghai Institute of Applied Physics, Chinese Academy of Sciences
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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].
