[gmx-users] bilayer problems and ffG45a

Sun Jun 12 00:00:43 CEST 2005

As far as I know, this original simulation was done at a temperature
323k (not 300k)
Both as the ref_t and for velocity generation.

Still, I'm not sure if that is the problem.

Good luck, Itai.

On 6/9/05, John Simms <JXS818 at bham.ac.uk> wrote:
> 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
> 
> 
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