[gmx-users] problem in pulling in gromacs 4.03
gmx3 at hotmail.com
Sun Apr 5 13:48:30 CEST 2009
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
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
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