[gmx-users] bilayer DMPC
Yiannis
ioannis.nicolis at free.fr
Wed May 14 10:37:17 CEST 2008
Search the list archive for rvdw with lipids, membranes or similar
keywords. Also look the rvdw values used in published work. There have
been discussions about balancing attractive and repulsive forces and
the cutoff values can have a strong influence on area.
And as others pointed, compare with the results obtained by the
authors from who your topology comes and the parameters they used.
(from the atom types you use I believe it comes from Tieleman's site?)
Ioannis
Le 14 mai 08 à 07:20, ANINDITA GAYEN a écrit :
> 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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