I have suffering from a problem with dmpc bilayer simulation at
300K
with oplsaa-berger combination that is showing area of 50nm2 after 1.5
ns from g_energy and g_traj. I have used half-epsilon double pairlist
method. the itp and mdp files are attached with. However editconf again
showing the correct box vectors after 1.5 ns, that was 6.176 6.167 9.008 the md.mdp file is title = bilayer MD DMPC PURE cpp = /usr/bin/cpp define = -DMPCPOSRES constraints = all-bonds constraint_algorithm= lincs lincs_order = 4 lincs_warnangle = 30 integrator = md dt = 0.002 ; ps ! nsteps = 1000000 ; total 100 ps. nstcomm = 1 comm-mode = linear nstxout = 500 nstvout = 500 nstfout = 500 nstenergy = 100 nstlist = 5 ns_type = grid rlist = 0.9 rcoulomb = 1.0 vdwtype = Cut-off rvdw = 2.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 coulombtype = PME pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = DMPC sol ref_t = 300 300 ; Pressure coupling is not on Pcoupl = berendsen tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 pcoupltype = semiisotropic ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 the changed ffoplsaachangemd.itp file portion is as [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_type mass charge ptype sigma epsilon LO 15.9994 0.000 A 0.296 0.87721 ;carbonyl O, OPLS LOM 15.9994 0.000 A 0.296 0.87721 ;carboxyl O, OPLS LNL 14.0067 0.000 A 0.325 0.7107 ;Nitrogen, OPLS LC 12.0110 0.000 A 0.37499 0.43967 ;Carbonyl C, OPLS LH1 13.0190 0.000 A 0.38002 0.33451 ;CH1, OPLS LH2 14.0270 0.000 A 0.3905 0.49353 ;CH2, OPLS LP 30.9738 0.000 A 0.37400 0.83653 ;phosphor, OPLS LOS 15.9994 0.000 A 0.29285 1.0158 ;ester oxygen, OPLS LP2 14.0270 0.000 A 0.29999 0.87809 ;RB CH2, Bergers LJ LP3 15.0350 0.000 A 0.396 0.568937 ;RB CH3, Bergers LJ LC3 15.0350 0.000 A 0.39601 0.67601 ;CH3, OPLS LC2 14.0270 0.000 A 0.3798 0.49419 ;CH2, OPLS with pair section [ pairtypes ] ; i j func sigma epsilon LO LO 1 0.29604 0.05482 LO LOM 1 0.29604 0.05482 LO opls_113 1 0.30632 0.04733 LO LNL 1 0.31018 0.04938 LO LC 1 0.33319 0.0388 LO LH1 1 0.33542 0.03383 LO LH2 1 0.34001 0.04111 LO LP 1 0.33275 0.05353 LO LOS 1 0.29799 0.0549 LO LP2 1 0.34237 0.03614 LO LP3 1 0.34239 0.04414 LO LC3 1 0.34238 0.04559 LO LC2 1 0.33539 0.04115 LOM LOM 1 0.29604 0.05482 LOM opls_113 1 0.30632 0.04733 LOM LNL 1 0.31018 0.04938 LOM LC 1 0.33319 0.0388 LOM LH1 1 0.33542 0.03383 LOM LH2 1 0.34001 0.04111 LOM LP 1 0.33275 0.05353 LOM LOS 1 0.29799 0.0549 LOM LP2 1 0.34237 0.03614 LOM LP3 1 0.34239 0.04414 LOM LC3 1 0.34238 0.04559 LOM LC2 1 0.33539 0.04115 opls_113 LNL 1 0.32095 0.04262 opls_113 LC 1 0.34478 0.03347 opls_113 LH1 1 0.34708 0.02921 opls_113 LH2 1 0.35181 0.0355 opls_113 LP 1 0.3443 0.04621 opls_113 LOS 1 0.30836 0.04737 opls_113 LP2 1 0.35427 0.0312 opls_113 LP3 1 0.35427 0.03812 opls_113 LC3 1 0.35428 0.03936 opls_113 LC2 1 0.34705 0.03551 LNL LNL 1 0.325 0.04446 LNL LC 1 0.34912 0.03492 LNL LH1 1 0.35145 0.03047 LNL LH2 1 0.35625 0.03703 LNL LP 1 0.34864 0.04822 LNL LOS 1 0.31224 0.04944 LNL LP2 1 0.35875 0.03254 LNL LP3 1 0.35877 0.03975 LNL LC3 1 0.35875 0.04106 LNL LC2 1 0.35139 0.03707 LC LC 1 0.37504 0.2743 LC LH1 1 0.37751 0.02395 LC LH2 1 0.3827 0.02908 LC LP 1 0.37452 0.03787 LC LOS 1 0.33542 0.03882 LC LP2 1 0.38535 0.25565 LC LP3 1 0.38539 0.03122 LC LC3 1 0.38537 0.03225 LC LC2 1 0.37751 0.02909 LH1 LH1 1 0.38004 0.02089 LH1 LH2 1 0.38525 0.02538 LH1 LP 1 0.37701 0.03305 LH1 LOS 1 0.33765 0.03388 LH1 LP2 1 0.38793 0.0223 LH1 LP3 1 0.38793 0.02724 LH1 LC3 1 0.38794 0.02814 LH1 LC2 1 0.38003 0.02539 LH2 LH2 1 0.39054 0.03082 LH2 LP 1 0.38218 0.04016 LH2 LOS 1 0.34227 0.04115 LH2 LP2 1 0.39324 0.0271 LH2 LP3 1 0.39328 0.03309 LH2 LC3 1 0.39324 0.03421 LH2 LC2 1 0.38523 0.03085 LP LP 1 0.37399 0.0523 LP LOS 1 0.33496 0.05359 LP LP2 1 0.38483 0.03529 LP LP3 1 0.38489 0.04306 LP LC3 1 0.38487 0.04451 LP LC2 1 0.37699 0.04017 LOS LOS 1 0.29998 0.05495 LOS LP2 1 0.34464 0.36185 LOS LP3 1 0.34468 0.04419 LOS LC3 1 0.34466 0.04564 LOS LC2 1 0.33762 0.04118 LP2 LP2 1 0.39596 0.02382 LP2 LP3 1 0.396 0.02909 LP2 LC3 1 0.39599 0.03005 LP2 LC2 1 0.38789 0.02712 LP3 LP3 1 0.39601 0.03556 LP3 LC3 1 0.396 0.03673 LP3 LC2 1 0.38792 0.03313 LC3 LC3 1 0.39599 0.03793 LC3 LC2 1 0.38791 0.03422 LC2 LC2 1 0.37998 0.03088 In the dmpcopls.itp, the [pairs] is repeated twice as per the double pairlist requirement. [ moleculetype ] ; name nrexcl DMPC 3 [ atoms ] ; id atype resnr resname aname cgnr charge mass 1 LC3 1 DMPC CN1 0 0.4000 15.0350 2 LC3 1 DMPC CN2 0 0.4000 15.0350 3 LC3 1 DMPC CN3 0 0.4000 15.0350 4 LNL 1 DMPC NTM 0 -0.5000 14.0067 5 LH2 1 DMPC CA 0 0.3000 14.0270 6 LC2 1 DMPC CB 1 0.4000 14.0270 7 LOS 1 DMPC OA 1 -0.8000 15.9994 8 LP 1 DMPC P 1 1.7000 30.9738 9 LOM 1 DMPC OB 1 -0.8000 15.9994 10 LOM 1 DMPC OC 1 -0.8000 15.9994 11 LOS 1 DMPC OD 1 -0.7000 15.9994 12 LC2 1 DMPC CC 2 0.4000 14.0270 13 LH1 1 DMPC CD 2 0.3000 13.0190 14 LOS 1 DMPC OE 2 -0.7000 15.9994 15 LC 1 DMPC C2A 2 0.7000 12.0110 16 LO 1 DMPC OF 2 -0.7000 15.9994 17 LP2 1 DMPC C2B 3 0.0000 14.0270 18 LP2 1 DMPC C2C 4 0.0000 14.0270 19 LP2 1 DMPC C2D 5 0.0000 14.0270 20 LP2 1 DMPC C2E 6 0.0000 14.0270 21 LP2 1 DMPC C2F 7 0.0000 14.0270 22 LP2 1 DMPC C2G 8 0.0000 14.0270 23 LP2 1 DMPC C2H 9 0.0000 14.0270 24 LP2 1 DMPC C2I 10 0.0000 14.0270 25 LP2 1 DMPC C2J 11 0.0000 14.0270 26 LP2 1 DMPC C2K 12 0.0000 14.0270 27 LP2 1 DMPC C2L 13 0.0000 14.0270 28 LP2 1 DMPC C2M 14 0.0000 14.0270 29 LP3 1 DMPC C2N 15 0.0000 15.0350 30 LC2 1 DMPC CE 18 0.5000 14.0270 31 LOS 1 DMPC OG 18 -0.7000 15.9994 32 LC 1 DMPC C1A 18 0.8000 12.0110 33 LO 1 DMPC OH 18 -0.6000 15.9994 34 LP2 1 DMPC C1B 19 0.0000 14.0270 35 LP2 1 DMPC C1C 20 0.0000 14.0270 36 LP2 1 DMPC C1D 21 0.0000 14.0270 37 LP2 1 DMPC C1E 22 0.0000 14.0270 38 LP2 1 DMPC C1F 23 0.0000 14.0270 39 LP2 1 DMPC C1G 24 0.0000 14.0270 40 LP2 1 DMPC C1H 25 0.0000 14.0270 41 LP2 1 DMPC C1I 26 0.0000 14.0270 42 LP2 1 DMPC C1J 27 0.0000 14.0270 43 LP2 1 DMPC C1K 28 0.0000 14.0270 44 LP2 1 DMPC C1L 29 0.0000 14.0270 45 LP2 1 DMPC C1M 30 0.0000 14.0270 46 LP3 1 DMPC C1N 31 0.0000 15.0350 [ bonds ] ; ai aj func b0 cb 1 4 1 0.14700E+00 0.37660E+06 2 4 1 0.14700E+00 0.37660E+06 3 4 1 0.14700E+00 0.37660E+06 4 5 1 0.14700E+00 0.37660E+06 5 6 1 0.15300E+00 0.33470E+06 6 7 1 0.14300E+00 0.33470E+06 7 8 1 0.16100E+00 0.25100E+06 8 9 1 0.14800E+00 0.33470E+06 8 10 1 0.14800E+00 0.33470E+06 8 11 1 0.16100E+00 0.25100E+06 11 12 1 0.14300E+00 0.33470E+06 12 13 1 0.15300E+00 0.33470E+06 13 14 1 0.14300E+00 0.33470E+06 14 15 1 0.13600E+00 0.37660E+06 15 16 1 0.12300E+00 0.50210E+06 15 17 1 0.15300E+00 0.33470E+06 17 18 1 0.15300E+00 0.33470E+06 18 19 1 0.15300E+00 0.33470E+06 19 20 1 0.15300E+00 0.33470E+06 20 21 1 0.15300E+00 0.33470E+06 21 22 1 0.15300E+00 0.33470E+06 22 23 1 0.15300E+00 0.33470E+06 23 24 1 0.15300E+00 0.33470E+06 24 25 1 0.15300E+00 0.33470E+06 25 26 1 0.15300E+00 0.33470E+06 26 27 1 0.15300E+00 0.33470E+06 27 28 1 0.15300E+00 0.33470E+06 28 29 1 0.15300E+00 0.33470E+06 13 30 1 0.15300E+00 0.33470E+06 30 31 1 0.14300E+00 0.33470E+06 31 32 1 0.13600E+00 0.37660E+06 32 33 1 0.12300E+00 0.50210E+06 32 34 1 0.15300E+00 0.33470E+06 34 35 1 0.15300E+00 0.33470E+06 35 36 1 0.15300E+00 0.33470E+06 36 37 1 0.15300E+00 0.33470E+06 37 38 1 0.15300E+00 0.33470E+06 38 39 1 0.15300E+00 0.33470E+06 39 40 1 0.15300E+00 0.33470E+06 40 41 1 0.15300E+00 0.33470E+06 41 42 1 0.15300E+00 0.33470E+06 42 43 1 0.15300E+00 0.33470E+06 43 44 1 0.15300E+00 0.33470E+06 44 45 1 0.15300E+00 0.33470E+06 45 46 1 0.15300E+00 0.33470E+06 [ pairs ] ;Here is the first copy ; ai aj func c6 c12 1 6 1 2 6 1 3 6 1 4 7 1 5 8 1 6 9 1 6 10 1 6 11 1 7 12 1 8 13 1 9 12 1 10 12 1 11 14 1 11 30 1 12 15 1 12 31 1 13 16 1 13 17 1 13 32 1 14 18 1 14 31 1 15 19 1 15 30 1 16 18 1 30 33 1 30 34 1 31 35 1 32 36 1 33 35 1 ; Here is the second copy. Only use this with the modified LJ-14 epsilon values 1 6 1 2 6 1 3 6 1 4 7 1 5 8 1 6 9 1 6 10 1 6 11 1 7 12 1 8 13 1 9 12 1 10 12 1 11 14 1 11 30 1 12 15 1 12 31 1 13 16 1 13 17 1 13 32 1 14 18 1 14 31 1 15 19 1 15 30 1 16 18 1 30 33 1 30 34 1 31 35 1 32 36 1 33 35 1 Thank you all Gromacs developers for upcomming suggestions |
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