[gmx-users] Pressure Coupling Problem
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 8 19:44:53 CEST 2009
Joe Joe wrote:
> Hi Chris,
>
> When I create the topology for the 4fs timestep I use pdb2gmx -vsite h.
> I set up the correct constraints. I've tested it and it conserves energy
> in NVE. I run all he sims with constraints=all-bonds. I am now running a
> single water box (800 water molecules) with 1s time steps and the volume
> keeps blowing up.
>
In addition to what Chris has been saying about constraints, consider your
pressure coupling settings themselves
Pcoupl = Berendsen
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 10
compressibility = 4.5e-5
ref_p = 1.01325
A 10-ps relaxation time for a system that is not necessarily well-equilibrated
is too weak, I think. Try 1.0 - 2.0 ps for tau_p. If your system is expanding
rapidly in as little as 5 ps, I would think you lack appropriate pressure
regulation.
-Justin
> Thanks,
>
> Ilya
>
>
> On Wed, Apr 8, 2009 at 8:37 AM, <chris.neale at utoronto.ca
> <mailto:chris.neale at utoronto.ca>> wrote:
>
> Hi Ilya,
>
> If you did include the entire mdp file then you have a time step of
> 4 fs and no constraints (other than water). For a timestep of 2 fs,
> you should constrain all-bonds (or some would say at least h-bonds)
> and for 4 fs then you should also constrain angles involving
> hydrogens (need a new .itp file for this).
>
> Can you try with a 1 fs timestep and see how it goes? Still, I am
> surprised that everything works out at NVT, but this is certainly
> worth the test.
>
> Do you have other systems running fine with these mdp options in NVT?
>
> Chris.
>
> -- original message --
>
> HI Chris,
>
> On Tue, Apr 7, 2009 at 9:31 PM, <chris.neale at utoronto.ca
> <http://utoronto.ca>> wrote:
>
> Hi Ilya,
>
> First thing that comes to mind is that it is strange to couple a
> coulombic
> switching function with PME. While this could possibly be done
> correctly, I
> doubt that it is in fact done in the way that you expect (i.e.
> correctly) in
> gromacs. In fact, I think that grompp/mdrun should probably
> throw an error
> here -- unless it is actually handled in the proper way, and a
> developer
> could help you here to figure out if you are indeed getting what
> you desire.
>
> coulombtype = PME
> rcoulomb-switch = .9
> rcoulomb = 1.0
>
>
>
> I am pretty sure gromacs ignores the rcoulomb-switch parameter in
> the case
> of PME but I will give it a try.
>
>
>
> However, it is not clear to me that this should cause a system to
> "continuously expand".
>
> Still, you do not give very good information about what you mean by
> "continuously expand". Can you please provide some information
> on that? e.g.
> amount of time and total volume change.
>
>
>
> My box density goes from ~1.0 to .5 in 5 ps with a compressibility
> of 5E-05.
> It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06.
> In both
> case the slope of density(t) is negative and never levels off.
>
>
>
> Chris
>
> -- original message --
>
> Hi
> I am having some pressure coupling issues. I have a fairly large
> protein/water system 400K+ atoms. It minimizes just fine (F <
> 1000). If I
> run NVE it conserves energy with appropriate parameter settings.
> If I run
> NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
> Rahman), the system just continuously expands. My parameters are as
> follows.
> Any ideas?
>
> Best,
>
> Ilya
>
> ;
> ; File 'mdout.mdp' was generated
> ; By user: relly (508)
> ; On host: master.simprota.com <http://master.simprota.com>
> ; At date: Fri Mar 6 20:17:33 2009
> ;
>
> ; VARIOUS PREPROCESSING OPTIONS
> ; Preprocessor information: use cpp syntax.
> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
> include =
> ; e.g.: -DI_Want_Cookies -DMe_Too
> define =
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.004
> ;nsteps = 250000
> nsteps = 2500000
> ; For exact run continuation or redoing part of a run
> ; Part index is updated automatically on checkpointing (keeps files
> separate)
> simulation_part = 1
> 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
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 0
> nstvout = 0
> nstfout = 0
>
> ; Output frequency for energies to log file and energy file
> nstlog = 10
> nstenergy = 10
> ; Output frequency and precision for xtc file
> nstxtcout = 250
> xtc-precision = 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps = protein
> ; Selection of energy groups
> energygrps =
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 5
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc = xyz
> periodic_molecules = no
> ; nblist cut-off
> rlist = 1.0
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> rcoulomb-switch = .9
> rcoulomb = 1.0
> ; Relative dielectric constant for the medium and the reaction field
> epsilon-r = 80
> epsilon_rf = 1
> ; Method for doing Van der Waals
> vdw-type = Switch
> ; cut-off lengths
> rvdw-switch = .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
> energygrp_table =
> ; 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 = 1.e-05
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl = V-rescale
> ; Groups to couple separately
> tc-grps = System
> ; Time constant (ps) and reference temperature (K)
> tau_t = 0.1
> ref_t = 298.0
> ; Pressure coupling
> Pcoupl = Berendsen
> Pcoupltype = Isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p = 10
> compressibility = 4.5e-5
> ref_p = 1.01325
> ; Scaling of reference coordinates, No, All or COM
> refcoord_scaling = No
> ; Random seed for Andersen thermostat
> andersen_seed = 815131
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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