[gmx-users] Re: Need Help about GROMACS.
Archana S Achalere
archana at chemeng.iisc.ernet.in
Tue May 18 13:37:43 CEST 2010
Thank you Dr. Justin for the reply.
Here are the details of my simulation.
I am simulating lipid bilayer (DPPC + water) where I
give equal and opposite force (along bilayer normal) on lipid and water molecules
I am using 128 DPPC and 3655 water. The .pdb file is taken from
Prof. Tieleman's page, University of Calgary.
I am trying to calculate water flux across the bilayer.
I apply the force by using nonequilibrium MD simulation option in .mdp
file, where the acceleration on two groups DPPC and water is given such
that the total force on each group would be equal and opposite.
I face two problems:
1. If I remove center of mass motion of whole System then the simulation
box starts suppressing along z direction (bilayer normal) and eventually
simulation terminates after few thousands of time steps.
2. If I give two groups DPPC and water for center of mass motion removal,
then bilayer moves along z direction (bilayer normal).
Please give me some direction to resolve this.
Here is my .mdp file:
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 15000000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps = System
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME-Switch
rcoulomb-switch = 0.9
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Switch
; cut-off lengths
rvdw-switch = 0.9
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = berendsen
; Groups to couple separately
tc-grps = DPPC SOL
; Time constant (ps) and reference temperature (K)
tau_t = 0.1 0.1
ref_t = 350 350
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; Non-equilibrium MD stuff
acc-grps = DPPC SOL
accelerate = 0.0 0.0 0.07 0.0 0.0 -0.1
cos-acceleration = 0
On Mon, 17 May 2010, Justin A. Lemkul wrote:
> Regardless of whether or not you've received a response, please keep all
> correspondence on the gmx-users list. I am not a private tutor. To what
> post are you referring? The list is fairly high-traffic, so if it's been a
> long time since you posted, don't continue to wait for a response. Post a
> new question, expanding upon your previous problem with any new details.
> You're more likely to get help if you demonstrate you are trying to help
> You're applying opposing forces between your lipids and water? That
> certainly sounds like a recipe for collapse. Perhaps if you can describe (by
> posting to the list) what you're doing, what you're hoping to accomplish, and
> what your .mdp settings are, you might get some more useful advice.
> Archana S Achalere wrote:
>> Dear Dr. Justin Lamkul,
>> I apologies that I am writing directly to you the query about my
>> simulation. As since long I have not got any response of my query posted on
>> I am simulating lipid bilayer (DPPC + water) where I give equal and
>> opposite force (along bilayer normal) on lipid and water molecules
>> I face two problems:
>> 1. If I remove center of mass motion of whole System then the simulation
>> box stars suppressing along z direction (bilayer normal) and eventually
>> simulation terminates after few thousands of time steps.
>> 2. If I give two groups DPPC and water for center of mass motion removal,
>> then bilayer moves along z direction (bilayer normal).
>> Could you please give me some direction how to resolve this.
>> Thank you.
>> Department of Chemical Engineering,
>> Indian Institute of Science,
>> Bangalore, India.
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