[gmx-users] Pressure Coupling Problem

Joe Joe ilchorny at gmail.com
Thu Apr 9 15:29:02 CEST 2009


So I got my small water box (800 waters) to behave stably with pressure
coupling after more minimization but I still can't get my large system to
work with pressure coupling. I tried minimizing but I can never get the Fmax
to be less 10^2, which is pretty normal for protein/water simulations of
large proteins, at least from my experience.  I have since run 400 ps NVT as
the system (425K atoms) is quite stable. The <P.E.> is 2E-05. Since I am
using 4fs time steps gromacs won't let me use a tau_p less than .4. Not sure
what else to do except run NVT, which is what I was going to do after I got
the density equilibrated. BTW, I am using octahedral PBC, but that should
not make a difference with respect to P coupling, should it? Below is my
whole mdp file. As a reminder my density in the system goes from 1.0 - .1 in
10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the
amount of time it takes for my system to expand increases but it still
expands.
;
;       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

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric                  = 0
ld-seed                  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol                    = 10
emstep                   = 0.01
; Max number of iterations in relax_shells
niter                    = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep                   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep               = 1000
nbfgscorr                = 10

; TEST PARTICLE INSERTION OPTIONS
rtpi                     = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 12500
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               = Protein SOL

; 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              = .8
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

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent         = No

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 2
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent       = 80
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha             = 1
gb_obc_beta              = 0.8
gb_obc_gamma             = 4.85
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
sa_surface_tension       = 2.092

; 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                    = 1.0
ref_t                    = 298.0
; Pressure coupling
Pcoupl                   = No
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

; OPTIONS FOR QMMM calculations
QMMM                     = no
; Groups treated Quantum Mechanically
QMMM-grps                =
; QM method
QMmethod                 =
; QMMM scheme
QMMMscheme               = normal
; QM basisset
QMbasis                  =
; QM charge
QMcharge                 =
; QM multiplicity
QMmult                   =
; Surface Hopping
SH                       =
; CAS space options
CASorbitals              =
CASelectrons             =
SAon                     =
SAoff                    =
SAsteps                  =
; Scale factor for MM charges
MMChargeScaleFactor      = 1
; Optimization of QM subsystem
bOPT                     =
bTS                      =

; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing                =
; Number of time points to use for specifying annealing in each group
annealing_npoints        =
; List of times at the annealing points for each group
annealing_time           =
; Temp. at each annealing point, for each group.
annealing_temp           =

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = yes
gen_temp                 = 298.0
gen-seed                 = 173529

; OPTIONS FOR BONDS
constraints              = all-bonds
; Type of constraint algorithm
constraint-algorithm     = lincs
; Do not constrain the start configuration
continuation             = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 6
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter               = 2
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle          = 30
; Convert harmonic bonds to morse potentials
morse                    = no

; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl           =

; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for
Ewald
nwall                    = 0
wall_type                = 9-3
wall_r_linpot            = -1
wall_atomtype            =

; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull                     = no

; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre                    = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting          = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed              = no
disre-fc                 = 1000
disre-tau                = 0
; Output frequency for pair distances to energy file
nstdisreout              = 100
; Orientation restraints: No or Yes
orire                    = no
; Orientation restraints force constant and tau for time averaging
orire-fc                 = 0
orire-tau                = 0
orire-fitgrp             =
; Output frequency for trace(SD) and S to energy file
nstorireout              = 100
; Dihedral angle restraints: No or Yes
dihre                    = no
dihre-fc                 = 1000

; Free energy control stuff
free-energy              = no
init-lambda              = 0
delta-lambda             = 0
sc-alpha                 = 0
sc-power                 = 0
sc-sigma                 = 0.3
couple-moltype           =
couple-lambda0           = vdw-q
couple-lambda1           = vdw-q
couple-intramol          = no

; Non-equilibrium MD stuff
acc-grps                 =
accelerate               =
freezegrps               =
freezedim                =
cos-acceleration         = 0
deform                   =

; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x                      =
E-xt                     =
E-y                      =
E-yt                     =
E-z                      =
E-zt                     =



On Wed, Apr 8, 2009 at 1:00 PM, Joe Joe <ilchorny at gmail.com> wrote:

>
>
> On Wed, Apr 8, 2009 at 11:31 AM, Roland Schulz <roland at utk.edu> wrote:
>
>>
>>
>> On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe <ilchorny at gmail.com> wrote:
>>
>>> 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.
>>>
>>
>> It is indeed supported and does work correctly. But you have to set
>> coulombtype PME-Switch. mdp options says:
>> "This is mainly useful constant energy simulations. For constant
>> temperature simulations the advantage of improved energy conservation is
>> usually outweighed by the small loss in accuracy of the electrostatics. "
>>
>> Roland
>>
>
> Yes, my point was that when electrostatics = PME then Gromacs ignores  the
> rcoulomb-switch parameter.
>
>>
>>
>>
>>>
>>>>
>>>> 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
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>>
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use thewww
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090409/5313ad09/attachment.html>


More information about the gromacs.org_gmx-users mailing list