<table cellspacing='0' cellpadding='0' border='0' ><tr><td style='font: inherit;'><div id="yiv1446621241"><div id="yiv1073276985"><div id="yiv1709268203">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<br>
the md.mdp file is<br>
title = bilayer MD DMPC PURE<br>
cpp = /usr/bin/cpp<br>
define = -DMPCPOSRES<br>
constraints = all-bonds<br>
constraint_algorithm= lincs <br>
lincs_order = 4 <br>
lincs_warnangle = 30<br>
integrator = md<br>
dt
= 0.002 ; ps !<br>
nsteps
= 1000000 ; total 100 ps.<br>
nstcomm = 1<br>
comm-mode = linear<br>
nstxout = 500<br>
nstvout = 500<br>
nstfout = 500<br>
nstenergy = 100<br>
nstlist = 5<br>
ns_type = grid<br>
rlist = 0.9<br>
rcoulomb = 1.0<br>
vdwtype = Cut-off<br>
rvdw = 2.0<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
coulombtype = PME<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tau_t
= 0.1
0.1<br>
tc-grps
= DMPC sol<br>
ref_t
= 300
300<br>
; Pressure coupling is not on<br>
Pcoupl = berendsen<br>
tau_p
= 1.0
1.0<br>
compressibility = 4.5e-5 4.5e-5<br>
ref_p
= 1.0
1.0<br>
pcoupltype = semiisotropic<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
the changed ffoplsaachangemd.itp file portion is as<br>
[ atomtypes ]<br>
; full atom descriptions are available in ffoplsaa.atp<br>
; name bond_type mass
charge
ptype
sigma epsilon<br>
LO
15.9994
0.000 A
0.296 0.87721 ;carbonyl O,
OPLS<br>
LOM
15.9994
0.000 A
0.296 0.87721 ;carboxyl O,
OPLS<br>
LNL
14.0067
0.000 A
0.325 0.7107 ;Nitrogen, OPLS<br>
LC
12.0110
0.000 A
0.37499 0.43967 ;Carbonyl C, OPLS<br>
LH1
13.0190
0.000 A
0.38002 0.33451 ;CH1, OPLS<br>
LH2
14.0270
0.000 A
0.3905 0.49353 ;CH2, OPLS<br>
LP
30.9738
0.000 A
0.37400 0.83653 ;phosphor, OPLS<br>
LOS
15.9994
0.000 A
0.29285 1.0158 ;ester oxygen, OPLS<br>
LP2
14.0270
0.000 A
0.29999 0.87809 ;RB CH2, Bergers LJ<br>
LP3
15.0350
0.000 A
0.396 0.568937 ;RB CH3, Bergers LJ<br>
LC3
15.0350
0.000 A
0.39601 0.67601 ;CH3, OPLS<br>
LC2
14.0270
0.000 A
0.3798 0.49419 ;CH2, OPLS<br>
with pair section <br>
[ pairtypes ]<br>
; i j func sigma epsilon<br>
LO LO 1 0.29604 0.05482<br>
LO LOM 1 0.29604 0.05482 <br>
LO opls_113 1 0.30632 0.04733 <br>
LO LNL 1 0.31018 0.04938 <br>
LO LC 1 0.33319 0.0388 <br>
LO LH1 1 0.33542 0.03383 <br>
LO LH2 1 0.34001 0.04111 <br>
LO LP 1 0.33275 0.05353 <br>
LO LOS 1 0.29799 0.0549 <br>
LO LP2 1 0.34237 0.03614 <br>
LO LP3 1 0.34239 0.04414 <br>
LO LC3 1 0.34238 0.04559 <br>
LO LC2 1 0.33539 0.04115 <br>
LOM LOM 1 0.29604 0.05482 <br>
LOM opls_113 1 0.30632 0.04733 <br>
LOM LNL 1 0.31018 0.04938 <br>
LOM LC 1 0.33319 0.0388 <br>
LOM LH1 1 0.33542 0.03383 <br>
LOM LH2 1 0.34001 0.04111 <br>
LOM LP 1 0.33275 0.05353 <br>
LOM LOS 1 0.29799 0.0549 <br>
LOM LP2 1 0.34237 0.03614 <br>
LOM LP3 1 0.34239 0.04414 <br>
LOM LC3 1 0.34238 0.04559 <br>
LOM LC2 1 0.33539 0.04115 <br>
opls_113 LNL 1 0.32095 0.04262 <br>
opls_113 LC 1 0.34478 0.03347 <br>
opls_113 LH1 1 0.34708 0.02921 <br>
opls_113 LH2 1 0.35181 0.0355 <br>
opls_113 LP 1 0.3443 0.04621 <br>
opls_113 LOS 1 0.30836 0.04737 <br>
opls_113 LP2 1 0.35427 0.0312 <br>
opls_113 LP3 1 0.35427 0.03812 <br>
opls_113 LC3 1 0.35428 0.03936 <br>
opls_113 LC2 1 0.34705 0.03551 <br>
LNL LNL 1
0.325
0.04446 <br>
LNL LC 1 0.34912 0.03492 <br>
LNL LH1 1 0.35145 0.03047 <br>
LNL LH2 1 0.35625 0.03703 <br>
LNL LP 1 0.34864 0.04822 <br>
LNL LOS 1 0.31224 0.04944 <br>
LNL LP2 1 0.35875 0.03254 <br>
LNL LP3 1 0.35877 0.03975 <br>
LNL LC3 1 0.35875 0.04106 <br>
LNL LC2 1 0.35139 0.03707 <br>
LC LC 1
0.37504 0.2743 <br>
LC LH1 1 0.37751 0.02395 <br>
LC LH2 1 0.3827 0.02908 <br>
LC LP 1 0.37452 0.03787 <br>
LC LOS 1 0.33542 0.03882 <br>
LC LP2 1 0.38535 0.25565 <br>
LC LP3 1 0.38539 0.03122 <br>
LC LC3 1 0.38537 0.03225 <br>
LC LC2 1 0.37751 0.02909 <br>
LH1 LH1 1 0.38004 0.02089 <br>
LH1 LH2 1 0.38525 0.02538 <br>
LH1 LP 1 0.37701 0.03305 <br>
LH1 LOS 1 0.33765 0.03388 <br>
LH1 LP2 1 0.38793 0.0223 <br>
LH1 LP3 1 0.38793 0.02724 <br>
LH1 LC3 1 0.38794 0.02814 <br>
LH1 LC2 1 0.38003 0.02539 <br>
LH2 LH2 1 0.39054 0.03082 <br>
LH2 LP 1 0.38218 0.04016 <br>
LH2 LOS 1 0.34227 0.04115 <br>
LH2 LP2 1 0.39324 0.0271 <br>
LH2 LP3 1 0.39328 0.03309 <br>
LH2 LC3 1 0.39324 0.03421 <br>
LH2 LC2 1 0.38523 0.03085 <br>
LP LP 1 0.37399 0.0523 <br>
LP LOS 1 0.33496 0.05359 <br>
LP LP2 1 0.38483 0.03529 <br>
LP LP3 1 0.38489 0.04306 <br>
LP LC3 1 0.38487 0.04451 <br>
LP LC2 1 0.37699 0.04017 <br>
LOS LOS 1 0.29998 0.05495 <br>
LOS LP2 1 0.34464 0.36185 <br>
LOS LP3 1 0.34468 0.04419 <br>
LOS LC3 1 0.34466 0.04564 <br>
LOS LC2 1 0.33762 0.04118 <br>
LP2 LP2 1 0.39596 0.02382 <br>
LP2 LP3 1 0.396 0.02909 <br>
LP2 LC3 1 0.39599 0.03005 <br>
LP2 LC2 1 0.38789 0.02712 <br>
LP3 LP3 1 0.39601 0.03556 <br>
LP3 LC3 1 0.396 0.03673 <br>
LP3 LC2 1 0.38792 0.03313 <br>
LC3 LC3 1 0.39599 0.03793 <br>
LC3 LC2 1 0.38791 0.03422 <br>
LC2 LC2 1 0.37998 0.03088 <br>
In the dmpcopls.itp,<br>
the [pairs] is repeated twice as per the double pairlist requirement.<br>[ moleculetype ]<br>
<br>
; name nrexcl<br>
DMPC 3<br>
<br>
[ atoms ]<br>
; id atype resnr
resname aname cgnr
charge mass<br>
1
LC3 1
DMPC
CN1 0 0.4000 15.0350<br>
2
LC3 1
DMPC
CN2 0 0.4000 15.0350<br>
3
LC3 1
DMPC
CN3 0 0.4000 15.0350<br>
4
LNL 1
DMPC
NTM 0 -0.5000 14.0067<br>
5
LH2 1
DMPC
CA 0 0.3000 14.0270<br>
6
LC2 1
DMPC
CB 1 0.4000 14.0270<br>
7
LOS 1
DMPC
OA 1 -0.8000 15.9994<br>
8
LP 1
DMPC
P 1 1.7000 30.9738<br>
9
LOM 1
DMPC
OB 1 -0.8000 15.9994<br>
10
LOM 1
DMPC
OC 1 -0.8000 15.9994<br>
11
LOS 1
DMPC
OD 1 -0.7000 15.9994<br>
12
LC2 1
DMPC
CC 2 0.4000 14.0270<br>
13
LH1 1
DMPC
CD 2 0.3000 13.0190<br>
14
LOS 1
DMPC
OE 2 -0.7000 15.9994<br>
15
LC 1
DMPC
C2A 2 0.7000 12.0110<br>
16
LO 1
DMPC
OF 2 -0.7000 15.9994<br>
17
LP2 1
DMPC
C2B 3 0.0000 14.0270<br>
18
LP2 1
DMPC
C2C 4 0.0000 14.0270<br>
19
LP2 1
DMPC
C2D 5 0.0000 14.0270<br>
20
LP2 1
DMPC
C2E 6 0.0000 14.0270<br>
21
LP2 1
DMPC
C2F 7 0.0000 14.0270<br>
22
LP2 1
DMPC
C2G 8 0.0000 14.0270<br>
23
LP2 1
DMPC
C2H 9 0.0000 14.0270<br>
24
LP2 1
DMPC C2I
10 0.0000 14.0270<br>
25
LP2 1
DMPC C2J
11 0.0000 14.0270<br>
26
LP2 1
DMPC C2K
12 0.0000 14.0270<br>
27
LP2 1
DMPC C2L
13 0.0000 14.0270<br>
28
LP2 1
DMPC C2M
14 0.0000 14.0270<br>
29
LP3 1
DMPC C2N
15 0.0000 15.0350<br>
30
LC2 1
DMPC
CE 18 0.5000 14.0270<br>
31
LOS 1
DMPC
OG 18 -0.7000 15.9994<br>
32
LC 1
DMPC C1A
18 0.8000 12.0110<br>
33
LO 1
DMPC
OH 18 -0.6000 15.9994<br>
34
LP2 1
DMPC C1B
19 0.0000 14.0270<br>
35
LP2 1
DMPC C1C
20 0.0000 14.0270<br>
36
LP2 1
DMPC C1D
21 0.0000 14.0270<br>
37
LP2 1
DMPC C1E
22 0.0000 14.0270<br>
38
LP2 1
DMPC C1F
23 0.0000 14.0270<br>
39
LP2 1
DMPC C1G
24 0.0000 14.0270<br>
40
LP2 1
DMPC C1H
25 0.0000 14.0270<br>
41
LP2 1
DMPC C1I
26 0.0000 14.0270<br>
42
LP2 1
DMPC C1J
27 0.0000 14.0270<br>
43
LP2 1
DMPC C1K
28 0.0000 14.0270<br>
44
LP2 1
DMPC C1L
29 0.0000 14.0270<br>
45
LP2 1
DMPC C1M
30 0.0000 14.0270<br>
46
LP3 1
DMPC C1N
31 0.0000 15.0350<br>
<br>
[ bonds ]<br>
; ai
aj
func
b0 cb<br>
1
4 1 0.14700E+00 0.37660E+06<br>
2
4 1 0.14700E+00 0.37660E+06<br>
3
4 1 0.14700E+00 0.37660E+06<br>
4
5 1 0.14700E+00 0.37660E+06<br>
5
6 1 0.15300E+00 0.33470E+06<br>
6
7 1 0.14300E+00 0.33470E+06<br>
7
8 1 0.16100E+00 0.25100E+06<br>
8
9 1 0.14800E+00 0.33470E+06<br>
8
10 1 0.14800E+00 0.33470E+06<br>
8
11 1 0.16100E+00 0.25100E+06<br>
11 12 1 0.14300E+00 0.33470E+06<br>
12 13 1 0.15300E+00 0.33470E+06<br>
13 14 1 0.14300E+00 0.33470E+06<br>
14 15 1 0.13600E+00 0.37660E+06<br>
15 16 1 0.12300E+00 0.50210E+06<br>
15 17 1 0.15300E+00 0.33470E+06<br>
17 18 1 0.15300E+00 0.33470E+06<br>
18 19 1 0.15300E+00 0.33470E+06<br>
19 20 1 0.15300E+00 0.33470E+06<br>
20 21 1 0.15300E+00 0.33470E+06<br>
21 22 1 0.15300E+00 0.33470E+06<br>
22 23 1 0.15300E+00 0.33470E+06<br>
23 24 1 0.15300E+00 0.33470E+06<br>
24 25 1 0.15300E+00 0.33470E+06<br>
25 26 1 0.15300E+00 0.33470E+06<br>
26 27 1 0.15300E+00 0.33470E+06<br>
27 28 1 0.15300E+00 0.33470E+06<br>
28 29 1 0.15300E+00 0.33470E+06<br>
13 30 1 0.15300E+00 0.33470E+06<br>
30 31 1 0.14300E+00 0.33470E+06<br>
31 32 1 0.13600E+00 0.37660E+06<br>
32 33 1 0.12300E+00 0.50210E+06<br>
32 34 1 0.15300E+00 0.33470E+06<br>
34 35 1 0.15300E+00 0.33470E+06<br>
35 36 1 0.15300E+00 0.33470E+06<br>
36 37 1 0.15300E+00 0.33470E+06<br>
37 38 1 0.15300E+00 0.33470E+06<br>
38 39 1 0.15300E+00 0.33470E+06<br>
39 40 1 0.15300E+00 0.33470E+06<br>
40 41 1 0.15300E+00 0.33470E+06<br>
41 42 1 0.15300E+00 0.33470E+06<br>
42 43 1 0.15300E+00 0.33470E+06<br>
43 44 1 0.15300E+00 0.33470E+06<br>
44 45 1 0.15300E+00 0.33470E+06<br>
45 46 1 0.15300E+00 0.33470E+06<br>
<br>
[ pairs ]<br>
;Here is the first copy<br>
; ai
aj
func
c6 c12<br>
1 6 1<br>
2 6 1<br>
3 6 1<br>
4 7 1<br>
5 8 1<br>
6 9 1<br>
6 10 1<br>
6 11 1<br>
7 12 1<br>
8 13 1<br>
9 12 1<br>
10 12 1<br>
11 14 1<br>
11 30 1<br>
12 15 1<br>
12 31 1<br>
13 16 1<br>
13 17 1<br>
13 32 1<br>
14 18 1<br>
14 31 1<br>
15 19 1<br>
15 30 1<br>
16 18 1<br>
30 33 1<br>
30 34 1<br>
31 35 1<br>
32 36 1<br>
33 35 1<br>
; Here is the second copy. Only use this with the modified LJ-14 epsilon values<br>
1 6 1<br>
2 6 1<br>
3 6 1<br>
4 7 1<br>
5 8 1<br>
6 9 1<br>
6 10 1<br>
6 11 1<br>
7 12 1<br>
8 13 1<br>
9 12 1<br>
10 12 1<br>
11 14 1<br>
11 30 1<br>
12 15 1<br>
12 31 1<br>
13 16 1<br>
13 17 1<br>
13 32 1<br>
14 18 1<br>
14 31 1<br>
15 19 1<br>
15 30 1<br>
16 18 1<br>
30 33 1<br>
30 34 1<br>
31 35 1<br>
32 36 1<br>
33 35 1<br>
Thank you all Gromacs developers for upcomming suggestions<br>
<br>
<br>
</div></div></div></td></tr></table><br>
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