[gmx-users] 1-4 Scaling Problem?
Chris Neale
chris.neale at utoronto.ca
Mon May 26 17:28:43 CEST 2008
>Dear Sir,
>
>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.
Note added at the end: Some of your topology parameters are incorrect.
That is likely the source of your problems. However, I left what I had
already written prior to discovering those errors in case your problems
persist...
Can you provide information about the standard deviation of the
SA/lipid? Better yet, make a plot and post it on photobucket and then
link that image to your next gromacs mailing list post.
Thank you for providing the information that experimental is 59.6A. What
did Tieleman report? I have run his POPC with the .mdp options stated in
the associated paper (LRLJ at 2.0nm) and found the area per lipid to
shrink immediately. I concluded from that test that, for that one paper
at least, either the methods section was not entirely correct, or the
ambiguous way in which the type of pressure coupling was explained led
me to do pressure coupling differently than they did (I used semiisotropic).
Therefore, I suggest that you first determine two things:
1) Look at the DMPC paper and figure out what area per lipid they report
(and what the standard deviations are for that value). If they also
report 55A from their simulations then
2) Since you have no protein, revert back prior to simple method of
including lipid.itp via ffgmx and see what you get. I have tested POPC
and DPPC and verified that I get the same values either with the above
mentioned protocol or with the half-epsilon-double-pairlist method (for
DPPC, see the .pdf that I posted wrt the method
http://www.pomeslab.com/files/lipidCombinationRules.pdf). If you get the
correct value via ffgmx and lipid.itp then you know that the problem
lies with your topology. Otherwise, you can look to the .mdp files.
>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.
Even 5ns is not enough for equilibration. Run longer, it should not be
very expensive to get >40ns. Check the plot at the bottom of that .pdf
that I mentioned to see what the area/lipid fluctuations can look like.
>
>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
I seriously hope that it doesn't matter, but I use nstlist = 10. You
could try that just to see if the difference is there, and remember that
if it is, this would make my simulations incorrect and yours correct.
>
>
>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
Aha! Some of the above values are incorrect. For example, LC3 should
read 0.3960142 and 0.606494
where you have 0.39601 0.67601. The trailing decimals are probably
not essential, but a difference
of >10% in the value of epsilon is sure to cause you headaches.
You also have incorrect values above for LOS and LP2, and perhaps others
but I stopped checking at this
point. Strangely, you have the correct LO-LC3 and LC3-LC3 values in the
[pairtypes] section below. I suggest that
you entirely remake this file and be very sure that you have done it
correctly.
Chris.
> .......................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
>
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