[gmx-users] Pressure Coupling Problem
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Wed Apr 8 18:18:29 CEST 2009
You say "I run all he sims with constraints=all-bonds", but I don't
see that in the mdp options that you provided. I even put your text in
a file and grepped for it just to be sure. Did you only give us a
partial mdp file?
Try adding this to your mdp file:
constraints = all-bonds ; REMOVE_FOR_EM
constraint_algorithm= lincs ; REMOVE_FOR_EM
lincs-iter = 1 ; REMOVE_FOR_EM
lincs-order = 6 ; REMOVE_FOR_EM
see, for example,
http://www.gromacs.org/pipermail/gmx-users/2008-October/037545.html
http://www.gromacs.org/pipermail/gmx-users/2008-November/037673.html
--- original message ---
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.
Thanks,
Ilya
On Wed, Apr 8, 2009 at 8:37 AM, <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> 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
>> ; 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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>
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