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
Planet Earth is in the hot seat. Know more.
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
