[gmx-users] 1-4 Scaling Problem?
Xavier Periole
X.Periole at rug.nl
Sat May 24 16:44:23 CEST 2008
> I am sufferering from a dmpc-bilayer-area shrinking problem. The fact is the
>experimental area at 300K is 59.6A2, where I am always getting 54A2 or 55A2
>area. The dmpc_npat.pdb along with lipi.itp and dmpc.itp was taken from the
>Tieleman's site, and I tried to modify these with half-epsilon double
>pairlist method to combine OPLS-BERGER.
The OPLS-Berger Lipids use a cutoff for vdW a bit smaller than the 1.4 nm
you use! try 1.2 and 1.0 nm you have a larger are per lipid, which does
not really mean you have a better representation of the lipids but your
area will be more reasonable.
>
> I am doing an initial minimisation (4500 steps with emtop 100) with flexible
>SPC and then turing on SETTLE and LINCS i am doing a pr-dynamics for 250ps
>and then MD run for 5ns. In the pr-dynamics, the area is around the original,
>but after starting MD, the area starts shrinking in 50ps only, and become
>continuous near 54A2. I know, 500ps is not sufficient for equilibration but
>the area shows no sign to again increase.
>
> The pr.mdp is:
> title = bilayer MD DMPC POSRES PURE
> cpp = /usr/bin/cpp
> define = -DDMPCPOSRES
> constraints = all-bonds
> constraint_algorithm= lincs
> lincs_order = 4
> lincs_warnangle = 30
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 125000 ; total 100 ps.
> nstcomm = 1
> comm-mode = linear
> nstxout = 5000
> nstvout = 5000
> nstfout = 5000
> nstenergy = 1000
> nstlist = 5
> ns_type = grid
> rlist = 0.9
> rcoulomb = 0.9
> vdwtype = Cut-off
> rvdw = 1.4
> 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 = 4.0 4.0
> 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 md.mdp file is:
>
> title = bilayer MD DMPC PURE
> cpp = /usr/bin/cpp
> constraints = all-bonds
> constraint_algorithm= lincs
> lincs_order = 4
> lincs_warnangle = 30
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 2500000 ; total 100 ps.
> nstcomm = 1
> comm-mode = linear
> nstxout = 5000
> nstvout = 5000
> nstfout = 5000
> nstenergy = 1000
> nstlist = 5
> ns_type = grid
> rlist = 0.9
> rcoulomb = 0.9
> vdwtype = Cut-off
> rvdw = 1.4
> 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 = 4.0 4.0
> 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 ffoplsaamd.itp is:
> #define _FF_OPLS
> #define _FF_OPLSAA
>
> ; This force field uses a format that requires Gromacs 3.1.4 or later.
> ;
> ; References for the OPLS-AA force field:
> ;
> ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,
> ; J. Am. Chem. Soc. 118, 11225-11236 (1996).
> ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).
> ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059
>(1998).
> ; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999).
> ; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001).
> ; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125
>(2001)..
> ; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J.
>Phys.. Chem. B 105, 6474 (2001).
> ;
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 3 yes 0.5 0.5
>
> #include "ffoplsaanbmd.itp"
> #include "ffoplsaabon.itp"
>
> the ffoplsaanbmd.itp is:
>
> [ atomtypes ]
> ; full atom descriptions are available in ffoplsaa.atp
> ; name bond_type mass charge ptype sigma epsilon
> LO LO 1 15.9994 0.000 A 0.296 0.87721
> ;carbonyl O, OPLS
> LOM LOM 1 15.9994 0.000 A 0.296 0.87721
> ;carboxyl O, OPLS
> LNL LNL 1 14.0067 0.000 A 0.325 0.7107
> ;Nitrogen, OPLS
> LC LC 1 12.0110 0.000 A 0.37499 0.43967
> ;Carbonyl C, OPLS
> LH1 LH1 1 13.0190 0.000 A 0.38002 0.33451
> ;CH1, OPLS
> LH2 LH2 1 14.0270 0.000 A 0.3905 0.49353
> ;CH2, OPLS
> LP LP 1 30.9738 0.000 A 0.37400 0.83653
> ;phosphor, OPLS
> LOS LOS 1 15.9994 0.000 A 0.29285 1.0158
> ;ester oxygen, OPLS
> LP2 LP2 1 14.0270 0.000 A 0.29999 0.87809 ;RB
>CH2, Bergers LJ
> LP3 LP3 1 15.0350 0.000 A 0.396 0.568937 ;RB
>CH3, Bergers LJ
> LC3 LC3 1 15.0350 0.000 A 0.39601 0.67601
> ;CH3, OPLS
> LC2 LC2 1 14.0270 0.000 A 0.3798 0.49419
> ;CH2, OPLS
> .......................OPLS lines................................
>
> [ 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
>
>
> [ dihedraltypes ]
> LP2 LP2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
> LH2 LH2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
>
> the dmpcopls.itp is:
>
> [ 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
>
> [ angles ]
> ; ai aj ak func t0 ct
> 1 4 2 1 0.10950E+03 0.46020E+03
> 1 4 3 1 0.10950E+03 0.46020E+03
> 1 4 5 1 0.10950E+03 0.46020E+03
> 2 4 3 1 0.10950E+03 0.46020E+03
> 2 4 5 1 0.10950E+03 0.46020E+03
> 3 4 5 1 0.10950E+03 0.46020E+03
> 4 5 6 1 0.10950E+03 0.46020E+03
> 5 6 7 1 0.10950E+03 0.46020E+03
> 6 7 8 1 0.12000E+03 0.39750E+03
> 7 8 9 1 0.10950E+03 0.39750E+03
> 7 8 10 1 0.10950E+03 0.39750E+03
> 7 8 11 1 0.10300E+03 0.39750E+03
> 9 8 10 1 0.12000E+03 0.58580E+03
> 9 8 11 1 0.10950E+03 0.39750E+03
> 10 8 11 1 0.10950E+03 0.39750E+03
> 8 11 12 1 0.12000E+03 0.39750E+03
> 11 12 13 1 0.11100E+03 0.46020E+03
> 12 13 14 1 0.10950E+03 0.46020E+03
> 12 13 30 1 0.10950E+03 0.46020E+03
> 14 13 30 1 0.10950E+03 0.46020E+03
> 13 14 15 1 0.12000E+03 0.41840E+03
> 14 15 16 1 0.12400E+03 0.50210E+03
> 14 15 17 1 0.11500E+03 0.50210E+03
> 16 15 17 1 0.12100E+03 0.50210E+03
> 15 17 18 1 0.11100E+03 0.46020E+03
> 17 18 19 1 0.11100E+03 0.46020E+03
> 18 19 20 1 0.11100E+03 0.46020E+03
> 19 20 21 1 0.11100E+03 0.46020E+03
> 20 21 22 1 0.11100E+03 0.46020E+03
> 21 22 23 1 0.11100E+03 0.46020E+03
> 22 23 24 1 0.11100E+03 0.46020E+03
> 23 24 25 1 0.11100E+03 0.46020E+03
> 24 25 26 1 0.11100E+03 0.46020E+03
> 25 26 27 1 0.11100E+03 0.46020E+03
> 26 27 28 1 0.11100E+03 0.46020E+03
> 27 28 29 1 0.11100E+03 0.46020E+03
> 13 30 31 1 0.11100E+03 0.46020E+03
> 30 31 32 1 0.12000E+03 0.41840E+03
> 31 32 33 1 0.12400E+03 0.50210E+03
> 31 32 34 1 0.11500E+03 0.50210E+03
> 33 32 34 1 0.12100E+03 0.50210E+03
> 32 34 35 1 0.11100E+03 0.46020E+03
> 34 35 36 1 0.11100E+03 0.46020E+03
> 35 36 37 1 0.11100E+03 0.46020E+03
> 36 37 38 1 0.11100E+03 0.46020E+03
> 37 38 39 1 0.11100E+03 0.46020E+03
> 38 39 40 1 0.11100E+03 0.46020E+03
> 39 40 41 1 0.11100E+03 0.46020E+03
> 40 41 42 1 0.11100E+03 0.46020E+03
> 41 42 43 1 0.11100E+03 0.46020E+03
> 42 43 44 1 0.11100E+03 0.46020E+03
> 43 44 45 1 0.11100E+03 0.46020E+03
> 44 45 46 1 0.11100E+03 0.46020E+03
>
> [ dihedrals ]
> ; These are the improper dihedrals
> ; ai aj ak al func q0 cq
> 13 14 30 12 2 0.35264E+02 0.33470E+03
> 15 14 17 16 2 0.00000E+00 0.16740E+03
> 32 31 34 33 2 0.00000E+00 0.16740E+03
>
> [ dihedrals ]
> ; These are the proper dihedrals
> ; ai aj ak al func phi0 cphi mult
> 1 4 5 6 1 0.00000E+00 0.37656E+01 3
> 4 5 6 7 1 0.00000E+00 0.58576E+01 3
> 5 6 7 8 1 0.00000E+00 0.37656E+01 3
> 6 7 8 11 1 0.00000E+00 0.10460E+01 3
> 7 8 11 12 1 0.00000E+00 0.10460E+01 3
> 8 11 12 13 1 0.00000E+00 0.37656E+01 3
> 11 12 13 14 1 0.00000E+00 0.20920E+01 2
> 12 13 14 15 1 0.00000E+00 0.37656E+01 3
> 13 14 15 17 1 0.18000E+03 0.16736E+02 2
> 14 15 17 18 1 0.00000E+00 0.41840E+00 6
> 15 17 18 19 1 0.00000E+00 0.58576E+01 3
> 17 18 19 20 3
> 18 19 20 21 3
> 19 20 21 22 3
> 20 21 22 23 3
> 21 22 23 24 3
> 22 23 24 25 3
> 23 24 25 26 3
> 24 25 26 27 3
> 25 26 27 28 3
> 26 27 28 29 3
> 14 13 30 31 1 0.00000E+00 0.20920E+01 2
> 13 30 31 32 1 0.00000E+00 0.37656E+01 3
> 30 31 32 34 1 0.18000E+03 0.16736E+02 2
> 31 32 34 35 1 0.00000E+00 0.41840E+00 6
> 32 34 35 36 1 0.00000E+00 0.58576E+01 3
> 34 35 36 37 3
> 35 36 37 38 3
> 36 37 38 39 3
> 37 38 39 40 3
> 38 39 40 41 3
> 39 40 41 42 3
> 40 41 42 43 3
> 41 42 43 44 3
> 42 43 44 45 3
> 43 44 45 46 3
>
> #ifdef DMPC_POSRES
> ; position restraints for DMPC
> [ position_restraints ]
> ; atom type fx fy fz
> 1 1 1000.0 1000.0 1000.0
> 2 1 1000.0 1000.0 1000.0
> 3 1 1000.0 1000.0 1000.0
> 4 1 1000.0 1000.0 1000.0
> 5 1 1000.0 1000.0 1000.0
> 6 1 1000.0 1000.0 1000.0
> 7 1 1000.0 1000.0 1000.0
> 8 1 1000.0 1000.0 1000.0
> 9 1 1000.0 1000.0 1000.0
> 10 1 1000.0 1000.0 1000.0
> 11 1 1000.0 1000.0 1000.0
> 12 1 1000.0 1000.0 1000.0
> 13 1 1000.0 1000.0 1000.0
> 14 1 1000.0 1000.0 1000.0
> 15 1 1000.0 1000.0 1000.0
> 16 1 1000.0 1000.0 1000.0
> 17 1 1000.0 1000.0 1000.0
> 18 1 1000.0 1000.0 1000.0
> 19 1 1000.0 1000.0 1000.0
> 20 1 1000.0 1000.0 1000.0
> 21 1 1000.0 1000.0 1000.0
> 22 1 1000.0 1000.0 1000.0
> 23 1 1000.0 1000.0 1000.0
> 24 1 1000.0 1000.0 1000.0
> 25 1 1000.0 1000.0 1000.0
> 26 1 1000.0 1000.0 1000.0
> 27 1 1000.0 1000.0 1000.0
> 28 1 1000.0 1000.0 1000.0
> 29 1 1000.0 1000.0 1000.0
> 30 1 1000.0 1000.0 1000.0
> 31 1 1000.0 1000.0 1000.0
> 32 1 1000.0 1000.0 1000.0
> 33 1 1000.0 1000.0 1000.0
> 34 1 1000.0 1000.0 1000.0
> 35 1 1000.0 1000.0 1000.0
> 36 1 1000.0 1000.0 1000.0
> 37 1 1000.0 1000.0 1000.0
> 38 1 1000.0 1000.0 1000.0
> 39 1 1000.0 1000.0 1000.0
> 40 1 1000.0 1000.0 1000.0
> 41 1 1000.0 1000.0 1000.0
> 42 1 1000.0 1000.0 1000.0
> 43 1 1000.0 1000.0 1000.0
> 44 1 1000.0 1000.0 1000.0
> 45 1 1000.0 1000.0 1000.0
> 46 1 1000.0 1000.0 1000.0
> #endif
>
> Is my 1-4 scaling correct? I am confused about my topologies. Please help.
>
>
> Ms. Anindita Gayen
>
> C/O Dr. Chaitali Mukhopadhyay
>
> Senior Research Fellow
>
> University of Calcutta
>
>
> Best Jokes, Best Friends, Best Food and more. Go to
>http://in.promos.yahoo.com/groups/bestofyahoo/
>
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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