[gmx-users] RE: problem in pulling in gromacs 4.03
schlesi at uni-mainz.de
Mon Apr 6 13:26:28 CEST 2009
Other then to use 4.0.4, i would try to change the simulation-time, the
force-constant of the spring (pull_k1) and the pulling velocity
(pull_rate1). You have both a low force-constant and a slow pulling
velocity, with a simulation-time around 500ps it is possible that only
see the protein vibrating, because it needs more time. So best would
probably to increase 'pull_k1' and 'pull_rate1' and simulate longer.
> I think this is a bug in 4.0.3.
> Please switch to 4.0.4.
> Date: Sat, 4 Apr 2009 22:00:44 +0530
> From: polley.anirban at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] problem in pulling in gromacs 4.03
> Dear sir,
> I want to pull a small protein molecule (GPI) which is inserted on the upper layer of the bilayer. So, I applied pull = umbrella, where umbrella potential is used between center of mass of reference group and that of pulled group. Now, as I want to pull the protein from the lipid bilayer membrane, I use the whole molecule of protein as pulled group and the whole patch of bilayer as a reference group because I thought that though I write the whole patch of bilayer as a reference group, the pull will occur w.r.t. the center of mass of the reference group. It will create no problem. Similarly, I did for the whole protein as a pulled group.
> I tried the pull_geometry as all distance, direction, position and it does not give any error during simulation. But, when I saw the whole trajectory in VMD, then I saw that the protein did not come out by the pulling. It is just vibrating at the same position.
> When I ran the simulation in NVT ensemble, the bilayer still retain its structure but when I ran it in NPT ensemble, it created crazy things, water entered inside, lipids became shrinked and so on.
> Can you please help me and tell me how to do it? I am eagerly waiting for your help.
> title = lipid bilayer in water
> cpp = /lib/cpp
> integrator = sd ; stochastic dynamics -> Langevin!
> ld_seed = -1 ; random seed for sd
> dt = 0.002 ; ps !
> nsteps = 250000 ; total 500 ps
> nstcomm = 1 ; freq. for cm-motion removal
> tinit = 0 ; starting time (ps)
> constraints = all-bonds ; constraint for all bond lengths
> constraint_algorithm = lincs ; default
> lincs_order = 4 ; default
> nstxout = 5000 ; T(x_out) 10 ps
> nstvout = 5000 ; T(v_out) 10 ps
> nstfout = 0 ; T(f_out)
> nstlog = 250 ; energies to log (0.5 ps)
> nstenergy = 250 ; energies to energy file
> ns_type = grid ; nl type
> nstlist = 10 ; Freq. to update neighbour list
> rlist = 1.0 ; nm (cutoff for short-range nl)
> coulombtype = PME ;Reaction-Field ; Coulomb interactions
> rcoulomb = 1.0 ;2.0 ; nm (Coulomb cut-off!!)
> epsilon_r = 80.0 ; dielectric constant for reaction field
> vdwtype = Cut-off ; Wan der Waals interactions
> rvdw = 1.0 ; nm (LJ cut-off)
> optimize_fft = yes
> ; Temperature coupling
> Tcoupl = no ; no effect when integrator = sd
> tc-grps = DPP SM CHOL SOL GPI
> tau_t = 0.1 0.1 0.1 0.1 0.1
> ref_t = 310 310 310 310 310
> ; Pressure coupling
> Pcoupl = no
> ;Pcoupl = berendsen
> Pcoupltype = semiisotropic
> tau_p = 1.0 1.0 ; ps
> compressibility = 4.5e-5 4.5e-5 ; 1/bar (water: 1 atm, 300 K)
> ref_p = 1.0 1.0 ; bar
> ; Generate velocites in the beginning
> gen_vel = yes
> gen_temp = 310.0
> gen_seed = 173529
> pull = umbrella
> pull_geometry = direction
> pull_start = yes
> pull_ngroups = 1
> pull_group0 = DPP
> pull_group1 = GPI
> pull_dim = N N Y
> pull_k1 = 100
> ;pull_kB1 = 500
> pull_rate1 = 0.0005
> pull_vec1 = 0 0 1
> pull_init1 = 0.0
> pull_nstxout = 1
> Thanking you,
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