[gmx-users] bilayer problems and ffG45a

Thu Jun 9 20:57:47 CEST 2005

Hi All,
I am having a bit of trouble with the a membrane simulation. I am using the ffG45a3 forcefield from the contributions page but after 5ns the lipid surface area approaches 57 A^2, which is below what it should be. Has anyone used this forcefield? Below is my .mdp file and the top file for the a DPPC lipid, the origonal bilayer was from peter tielemans site (dppc64.pdb). 
If anyone has any suggestions...
Many Thanks
John 

title = dppc64

cpp = /lib/cpp

;Run Parameters

integrator = md

dt = 0.002 ; ps !

nsteps = 500000 

nstcomm = 1

nstxout = 5000

nstvout = 5000

nstfout = 0

nstlog = 100

nstenergy = 100

nstlist = 5

ns_type = grid

;Bonds

constraints = all-bonds

constraint_algorithm = Lincs

lincs_order = 4

;vdw

vdw_type = cut-off

rlist = 0.9

rvdw = 1.5

;Electrostatics

coulombtype = PME

fourierspacing = 0.12

rcoulomb = 0.9

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

Tcoupl = berendsen

tc-grps = DPP SOL 

tau_t = 0.1 0.1 

ref_t = 300 300 

; Energy monitoring

energygrps = DPP SOL 

; anisotropic pressure coupling is now on

Pcoupl = berendsen

Pcoupltype = anisotropic

tau_p = 5

compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0

ref_p = 1.01 1.01 1.01 1.01 1.01 1.01

; Generate velocites is on at 300 K.

gen_vel = no

gen_temp = 300.0

gen_seed = 173529

DispCorr = EnerPres

and the dppc.itp file

[ moleculetype ]

; Name nrexcl

DPP 3

[ atoms ]

; nr tyP8e resnr resid atom cgnr charge mass

1 CH3 1 DPP C1 0 0.4 15.035

2 CH3 1 DPP C2 0 0.4 15.035

3 CH3 1 DPP C3 0 0.4 15.035

4 NL 1 DPP N4 0 -0.5 14.0067

5 CH2 1 DPP C5 0 0.3 14.027

6 CH2 1 DPP C6 1 0.4 14.027

7 OA 1 DPP O7 1 -0.8 15.9994

8 P 1 DPP P8 1 1.7 30.9738

9 OM 1 DPP O9 1 -0.8 15.9994

10 OM 1 DPP O10 1 -0.8 15.9994

11 OA 1 DPP O11 1 -0.7 15.9994

12 CH2 1 DPP C12 2 0.4 14.027

13 CH1 1 DPP C13 2 0.3 13.019

14 OA 1 DPP O14 2 -0.7 15.9994

15 CH0 1 DPP C15 2 0.7 12.011

16 O 1 DPP O16 2 -0.7 15.9994

17 CH2 1 DPP C17 3 0 14.027

18 CH2 1 DPP C18 4 0 14.027

19 CH2 1 DPP C19 5 0 14.027

20 CH2 1 DPP C20 6 0 14.027

21 CH2 1 DPP C21 7 0 14.027

22 CH2 1 DPP C22 8 0 14.027

23 CH2 1 DPP C23 9 0 14.027

24 CH2 1 DPP C24 10 0 14.027

25 CH2 1 DPP C25 11 0 14.027

26 CH2 1 DPP C26 12 0 14.027

27 CH2 1 DPP C27 13 0 14.027

28 CH2 1 DPP C28 14 0 14.027

29 CH2 1 DPP C29 15 0 14.027

30 CH2 1 DPP C30 16 0 14.027

31 CH3 1 DPP C31 17 0 15.035

32 CH2 1 DPP C32 18 0.5 14.027

33 OA 1 DPP O33 18 -0.7 15.9994

34 CH0 1 DPP C34 18 0.8 12.011

35 O 1 DPP O35 18 -0.6 15.9994

36 CH2 1 DPP C36 19 0 14.027

37 CH2 1 DPP C37 20 0 14.027

38 CH2 1 DPP C38 21 0 14.027

39 CH2 1 DPP C39 22 0 14.027

40 CH2 1 DPP C40 23 0 14.027

41 CH2 1 DPP C41 24 0 14.027

42 CH2 1 DPP C42 25 0 14.027

43 CH2 1 DPP C43 26 0 14.027

44 CH2 1 DPP C44 27 0 14.027

45 CH2 1 DPP C45 28 0 14.027

46 CH2 1 DPP C46 29 0 14.027

47 CH2 1 DPP C47 30 0 14.027

48 CH2 1 DPP C48 31 0 14.027

49 CH2 1 DPP C49 32 0 14.027

50 CH3 1 DPP C50 33 0 15.035

[ bonds ]

; ai aj fu c0, c1, ...

31 30 2 0.1530 7.1500e+06 ; C31 C30

30 29 2 0.1530 7.1500e+06 ; C30 C29

29 28 2 0.1530 7.1500e+06 ; C29 C28

28 27 2 0.1530 7.1500e+06 ; C28 C27

27 26 2 0.1530 7.1500e+06 ; C27 C26

26 25 2 0.1530 7.1500e+06 ; C26 C25

25 24 2 0.1530 7.1500e+06 ; C25 C24

24 23 2 0.1530 7.1500e+06 ; C24 C23

23 22 2 0.1530 7.1500e+06 ; C23 C22

22 21 2 0.1530 7.1500e+06 ; C22 C21

21 20 2 0.1530 7.1500e+06 ; C21 C20

20 19 2 0.1530 7.1500e+06 ; C20 C19

19 18 2 0.1530 7.1500e+06 ; C19 C18

18 17 2 0.1530 7.1500e+06 ; C18 C17

17 15 2 0.1480 7.6400e+06 ; C17 C15

15 16 2 0.1230 1.6600e+07 ; C15 O16

15 14 2 0.1330 1.1800e+07 ; C15 O14

14 13 2 0.1430 8.1800e+06 ; O14 C13

13 12 2 0.1530 7.1500e+06 ; C13 C12

13 32 2 0.1530 7.1500e+06 ; C13 C32

12 11 2 0.1430 8.1800e+06 ; C12 O11

11 8 2 0.1610 4.8400e+06 ; O11 P8

8 9 2 0.1480 8.6000e+06 ; P8 O9

8 10 2 0.1480 8.6000e+06 ; P8 O10

8 7 2 0.1610 4.8400e+06 ; P8 O7

7 6 2 0.1430 8.1800e+06 ; O7 C6

6 5 2 0.1530 7.1500e+06 ; C6 C5

5 4 2 0.1470 8.7100e+06 ; C5 N4

4 2 2 0.1470 8.7100e+06 ; N4 C2

4 3 2 0.1470 8.7100e+06 ; N4 C3

4 1 2 0.1470 8.7100e+06 ; N4 C1

32 33 2 0.1430 8.1800e+06 ; C32 O33

33 34 2 0.1330 1.1800e+07 ; O33 C34

34 35 2 0.1230 1.6600e+07 ; C34 O35

34 36 2 0.1480 7.6400e+06 ; C34 C36

36 37 2 0.1530 7.1500e+06 ; C36 C37

37 38 2 0.1530 7.1500e+06 ; C37 C38

38 39 2 0.1530 7.1500e+06 ; C38 C39

39 40 2 0.1530 7.1500e+06 ; C39 C40

40 41 2 0.1530 7.1500e+06 ; C40 C41

41 42 2 0.1530 7.1500e+06 ; C41 C42

42 43 2 0.1530 7.1500e+06 ; C42 C43

43 44 2 0.1530 7.1500e+06 ; C43 C44

44 45 2 0.1530 7.1500e+06 ; C44 C45

45 46 2 0.1530 7.1500e+06 ; C45 C46

46 47 2 0.1530 7.1500e+06 ; C46 C47

47 48 2 0.1530 7.1500e+06 ; C47 C48

48 49 2 0.1530 7.1500e+06 ; C48 C49

49 50 2 0.1530 7.1500e+06 ; C49 C50

[ pairs ]

; ai aj funct

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 32 1 

12 15 1 

12 33 1 

13 16 1 

13 17 1 

13 34 1 

14 18 1 

14 33 1 

15 19 1 

15 32 1 

16 18 1 

32 35 1 

32 36 1 

33 37 1 

34 38 1 

35 37 1 

[ angles ]

; ai aj ak fu c0, c1, ...

31 30 29 2 111.00 530.00 ; C31 C30 C29

30 29 28 2 111.00 530.00 ; C30 C29 C28

29 28 27 2 111.00 530.00 ; C29 C28 C27

28 27 26 2 111.00 530.00 ; C28 C27 C26

27 26 25 2 111.00 530.00 ; C27 C26 C25

26 25 24 2 111.00 530.00 ; C26 C25 C24

25 24 23 2 111.00 530.00 ; C25 C24 C23

24 23 22 2 111.00 530.00 ; C24 C23 C22

23 22 21 2 111.00 530.00 ; C23 C22 C21

22 21 20 2 111.00 530.00 ; C22 C21 C20

21 20 19 2 111.00 530.00 ; C21 C20 C19

20 19 18 2 111.00 530.00 ; C20 C19 C18

19 18 17 2 111.00 530.00 ; C19 C18 C17

18 17 15 2 111.00 530.00 ; C18 C17 C15

17 15 16 2 125.00 750.00 ; C17 C15 O16

17 15 14 2 113.00 545.00 ; C17 C15 O14

16 15 14 2 122.00 700.00 ; O16 C15 O14

15 14 13 2 117.00 635.00 ; C15 O14 C13

14 13 12 2 109.50 520.00 ; O14 C13 C12

14 13 32 2 109.50 520.00 ; O14 C13 C32

12 13 32 2 109.50 520.00 ; C12 C13 C32

13 12 11 2 111.00 530.00 ; C13 C12 O11

12 11 8 2 120.00 530.00 ; C12 O11 P8

11 8 9 2 109.60 450.00 ; O11 P8 O9

11 8 10 2 109.60 450.00 ; O11 P8 O10

11 8 7 2 103.00 420.00 ; O11 P8 O7

9 8 10 2 120.00 780.00 ; O9 P8 O10

9 8 7 2 109.60 450.00 ; O9 P8 O7

10 8 7 2 109.60 450.00 ; O10 P8 O7

8 7 6 2 120.00 530.00 ; P8 O7 C6

7 6 5 2 111.00 530.00 ; O7 C6 C5

6 5 4 2 111.00 530.00 ; C6 C5 N4

5 4 2 2 109.50 520.00 ; C5 N4 C2

5 4 3 2 109.50 520.00 ; C5 N4 C3

5 4 1 2 109.50 520.00 ; C5 N4 C1

2 4 3 2 109.50 520.00 ; C2 N4 C3

2 4 1 2 109.50 520.00 ; C2 N4 C1

3 4 1 2 109.50 520.00 ; C3 N4 C1

13 32 33 2 111.00 530.00 ; C13 C32 O33

32 33 34 2 117.00 635.00 ; C32 O33 C34

33 34 35 2 122.00 700.00 ; O33 C34 O35

33 34 36 2 113.00 545.00 ; O33 C34 C36

35 34 36 2 125.00 750.00 ; O35 C34 C36

34 36 37 2 111.00 530.00 ; C34 C36 C37

36 37 38 2 111.00 530.00 ; C36 C37 C38

37 38 39 2 111.00 530.00 ; C37 C38 C39

38 39 40 2 111.00 530.00 ; C38 C39 C40

39 40 41 2 111.00 530.00 ; C39 C40 C41

40 41 42 2 111.00 530.00 ; C40 C41 C42

41 42 43 2 111.00 530.00 ; C41 C42 C43

42 43 44 2 111.00 530.00 ; C42 C43 C44

43 44 45 2 111.00 530.00 ; C43 C44 C45

44 45 46 2 111.00 530.00 ; C44 C45 C46

45 46 47 2 111.00 530.00 ; C45 C46 C47

46 47 48 2 111.00 530.00 ; C46 C47 C48

47 48 49 2 111.00 530.00 ; C47 C48 C49

48 49 50 2 111.00 530.00 ; C48 C49 C50

[ dihedrals ]

; ai aj ak al fu c0, c1, m, ...

28 29 30 31 3 ; dih C28 C29 C30 C31

27 28 29 30 3 ; dih C27 C28 C29 C30

26 27 28 29 3 ; dih C26 C27 C28 C29

25 26 27 28 3 ; dih C25 C26 C27 C28

24 25 26 27 3 ; dih C24 C25 C26 C27

23 24 25 26 3 ; dih C23 C24 C25 C26

22 23 24 25 3 ; dih C22 C23 C24 C25

21 22 23 24 3 ; dih C21 C22 C23 C24

20 21 22 23 3 ; dih C20 C21 C22 C23

19 20 21 22 3 ; dih C19 C20 C21 C22

18 19 20 21 3 ; dih C18 C19 C20 C21

17 18 19 20 3 ; dih C17 C18 C19 C20

15 17 18 19 3 ; dih C15 C17 C18 C19

1 4 5 6 1 0.000 3.77 3 ; dih C1 N4 C5 C6

4 5 6 7 1 0.000 5.92 3 ; dih N4 C5 C6 O7

5 6 7 8 1 0.000 3.77 3 ; dih C5 C6 O7 P8

6 7 8 11 1 0.000 1.05 3 ; dih C6 O7 P8 O11

6 7 8 11 1 0.000 3.14 2 ; dih C6 O7 P8 O11

7 8 11 12 1 0.000 1.05 3 ; dih O7 P8 O11 C12

7 8 11 12 1 0.000 3.14 2 ; dih O7 P8 O11 C12

8 11 12 13 1 0.000 3.77 3 ; dih P8 O11 C12 C13

11 12 13 32 1 0.000 5.92 3 ; dih O11 C12 C13 C32

12 13 14 15 1 0.000 3.77 3 ; dih C12 C13 O14 C15

12 13 32 33 1 0.000 5.92 3 ; dih C12 C13 C32 O33

13 32 33 34 1 0.000 3.77 3 ; dih C13 C32 O33 C34

13 14 15 16 1 0.000 3.77 3 ; dih C13 O14 C15 O16

14 15 17 18 1 0.000 1.0 6 ; dih O14 C15 C17 C18

32 33 34 35 1 0.000 3.77 3 ; dih C32 O33 C34 O35

33 34 36 37 1 0.000 1.0 6 ; dih O33 C34 C36 C37

38 37 36 34 3 ; dih C38 C37 C36 C34

39 38 37 36 3 ; dih C39 C38 C37 C36

40 39 38 37 3 ; dih C40 C39 C38 C37

41 40 39 38 3 ; dih C41 C40 C39 C38

42 41 40 39 3 ; dih C42 C41 C40 C39

43 42 41 40 3 ; dih C43 C42 C41 C40

44 43 42 41 3 ; dih C44 C43 C42 C41

45 44 43 42 3 ; dih C45 C44 C43 C42

46 45 44 43 3 ; dih C46 C45 C44 C43

47 46 45 44 3 ; dih C47 C46 C45 C44

48 47 46 45 3 ; dih C48 C47 C46 C45

49 48 47 46 3 ; dih C49 C48 C47 C46

50 49 48 47 3 ; dih C50 C49 C48 C47

[ dihedrals ]

; ai aj ak al fu c0, c1, m, ...

13 32 12 14 2 35.26439 334.84617 ; imP8

15 14 17 16 2 0.0 167.42309 ; imP8

34 33 36 35 2 0.0 167.42309 ; imP8

#ifdef POSRES_LIPID

#include "lipid_posre.itp"

#endif