[gmx-users] Pressure Coupling Problem
Joe Joe
ilchorny at gmail.com
Wed Apr 8 21:57:48 CEST 2009
Yeah I only gave a partial. Tried to remove the QM params. I do use
constraints = all-bonds.
On Wed, Apr 8, 2009 at 9:18 AM, <chris.neale at utoronto.ca> wrote:
> 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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