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.<div>
<br></div><div><div>;</div><div>; File 'mdout.mdp' was generated</div><div>; By user: relly (508)</div><div>; On host: <a href="http://master.simprota.com">master.simprota.com</a></div><div>; At date: Fri Mar 6 20:17:33 2009</div>
<div>;</div><div><br></div><div>; VARIOUS PREPROCESSING OPTIONS</div><div>; Preprocessor information: use cpp syntax.</div><div>; e.g.: -I/home/joe/doe -I/home/mary/hoe</div><div>include =</div><div>; e.g.: -DI_Want_Cookies -DMe_Too</div>
<div>define =</div><div><br></div><div>; RUN CONTROL PARAMETERS</div><div>integrator = md</div><div>; Start time and timestep in ps</div><div>tinit = 0</div><div>dt = 0.004</div>
<div>;nsteps = 250000</div><div>nsteps = 2500000</div><div>; For exact run continuation or redoing part of a run</div><div>; Part index is updated automatically on checkpointing (keeps files separate)</div>
<div>simulation_part = 1</div><div>init_step = 0</div><div>; mode for center of mass motion removal</div><div>comm_mode = linear</div><div>; number of steps for center of mass motion removal</div>
<div>nstcomm = 1</div><div>; group(s) for center of mass motion removal</div><div>comm_grps = system</div><div><br></div><div>; LANGEVIN DYNAMICS OPTIONS</div><div>; Friction coefficient (amu/ps) and random seed</div>
<div>bd-fric = 0</div><div>ld-seed = 1993</div><div><br></div><div>; ENERGY MINIMIZATION OPTIONS</div><div>; Force tolerance and initial step-size</div><div>emtol = 10</div>
<div>emstep = 0.01</div><div>; Max number of iterations in relax_shells</div><div>niter = 20</div><div>; Step size (ps^2) for minimization of flexible constraints</div><div>fcstep = 0</div>
<div>; Frequency of steepest descents steps when doing CG</div><div>nstcgsteep = 1000</div><div>nbfgscorr = 10</div><div><br></div><div>; TEST PARTICLE INSERTION OPTIONS</div><div>rtpi = 0.05</div>
<div><br></div><div>; OUTPUT CONTROL OPTIONS</div><div>; Output frequency for coords (x), velocities (v) and forces (f)</div><div>nstxout = 12500</div><div>nstvout = 0</div><div>nstfout = 0</div>
<div>; Output frequency for energies to log file and energy file</div><div>nstlog = 10</div><div>nstenergy = 10</div><div>; Output frequency and precision for xtc file</div><div><div>nstxtcout = 250</div>
<div>xtc-precision = 1000</div><div>; This selects the subset of atoms for the xtc file. You can</div><div>; select multiple groups. By default all atoms will be written.</div><div>xtc-grps = protein</div>
<div>; Selection of energy groups</div><div>energygrps = Protein SOL</div><div><br></div><div>; NEIGHBORSEARCHING PARAMETERS</div><div>; nblist update frequency</div><div>nstlist = 5</div><div>
; ns algorithm (simple or grid)</div><div>ns_type = grid</div><div>; Periodic boundary conditions: xyz, no, xy</div><div>pbc = xyz</div><div>periodic_molecules = no</div><div>; nblist cut-off</div>
<div>rlist = 1.0</div><div><br></div><div>; OPTIONS FOR ELECTROSTATICS AND VDW</div><div>; Method for doing electrostatics</div><div>coulombtype = PME</div><div>rcoulomb-switch = .9</div>
<div>rcoulomb = 1.0</div><div>; Relative dielectric constant for the medium and the reaction field</div><div>epsilon-r = 80</div><div>epsilon_rf = 1</div><div>; Method for doing Van der Waals</div>
<div>vdw-type = Switch</div><div>; cut-off lengths</div><div>rvdw-switch = .8</div><div>rvdw = 1.0</div><div>; Apply long range dispersion corrections for Energy and Pressure</div>
<div>DispCorr = EnerPres</div><div>; Extension of the potential lookup tables beyond the cut-off</div><div>table-extension = 1</div><div>; Seperate tables between energy group pairs</div><div>energygrp_table =</div>
<div>; Spacing for the PME/PPPM FFT grid</div><div>fourierspacing = 0.12</div><div>; FFT grid size, when a value is 0 fourierspacing will be used</div><div>fourier_nx = 0</div><div>fourier_ny = 0</div>
<div>fourier_nz = 0</div><div>; EWALD/PME/PPPM parameters</div><div>pme_order = 4</div><div>ewald_rtol = 1.e-05</div><div>ewald_geometry = 3d</div><div>epsilon_surface = 0</div>
<div>optimize_fft = no</div><div><br></div><div>; IMPLICIT SOLVENT ALGORITHM</div><div>implicit_solvent = No</div><div><br></div><div>; GENERALIZED BORN ELECTROSTATICS</div><div>; Algorithm for calculating Born radii</div>
<div>gb_algorithm = Still</div><div>; Frequency of calculating the Born radii inside rlist</div><div>nstgbradii = 1</div><div><div>; Cutoff for Born radii calculation; the contribution from atoms</div>
<div>; between rlist and rgbradii is updated every nstlist steps</div><div>rgbradii = 2 </div><div>; Dielectric coefficient of the implicit solvent</div><div>gb_epsilon_solvent = 80</div><div>; Salt concentration in M for Generalized Born models</div>
<div>gb_saltconc = 0</div><div>; Scaling factors used in the OBC GB model. Default values are OBC(II)</div><div>gb_obc_alpha = 1</div><div>gb_obc_beta = 0.8</div><div>gb_obc_gamma = 4.85</div>
<div>; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA</div><div>; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.</div><div>sa_surface_tension = 2.092</div><div><br></div>
<div>; OPTIONS FOR WEAK COUPLING ALGORITHMS</div><div>; Temperature coupling</div><div>Tcoupl = V-rescale</div><div>; Groups to couple separately</div><div>tc-grps = System</div><div>; Time constant (ps) and reference temperature (K)</div>
<div>tau_t = 1.0</div><div>ref_t = 298.0</div><div>; Pressure coupling</div><div>Pcoupl = No</div><div>Pcoupltype = Isotropic</div><div>; Time constant (ps), compressibility (1/bar) and reference P (bar)</div>
<div>tau_p = 10 </div><div>compressibility = 4.5e-5</div><div>ref_p = 1.01325</div><div>; Scaling of reference coordinates, No, All or COM</div><div>refcoord_scaling = No</div>
<div>; Random seed for Andersen thermostat</div><div>andersen_seed = 815131</div><div><br></div><div>; OPTIONS FOR QMMM calculations</div><div>QMMM = no</div><div>; Groups treated Quantum Mechanically</div>
<div>QMMM-grps = </div><div>; QM method </div><div>QMmethod = </div><div>; QMMM scheme</div><div>QMMMscheme = normal</div><div>; QM basisset</div><div>QMbasis = </div>
<div>; QM charge</div><div>QMcharge = </div><div>; QM multiplicity</div><div>QMmult = </div><div>; Surface Hopping</div><div>SH =</div><div>; CAS space options </div>
<div>CASorbitals = </div><div>CASelectrons =</div><div>SAon = </div><div>SAoff = </div><div>SAsteps = </div><div>; Scale factor for MM charges</div>
<div>MMChargeScaleFactor = 1</div><div><div>; Optimization of QM subsystem</div><div>bOPT =</div><div>bTS =</div><div><br></div><div>; SIMULATED ANNEALING</div><div>; Type of annealing for each temperature group (no/single/periodic)</div>
<div>annealing =</div><div>; Number of time points to use for specifying annealing in each group</div><div>annealing_npoints =</div><div>; List of times at the annealing points for each group</div><div>
annealing_time =</div><div>; Temp. at each annealing point, for each group.</div><div>annealing_temp =</div><div><br></div><div>; GENERATE VELOCITIES FOR STARTUP RUN</div><div>gen_vel = yes</div>
<div>gen_temp = 298.0</div><div>gen-seed = 173529</div><div><br></div><div>; OPTIONS FOR BONDS</div><div>constraints = all-bonds</div><div>; Type of constraint algorithm</div><div>
constraint-algorithm = lincs</div><div>; Do not constrain the start configuration</div><div>continuation = no</div><div>; Use successive overrelaxation to reduce the number of shake iterations</div><div>Shake-SOR = no</div>
<div>; Relative tolerance of shake</div><div>shake-tol = 0.0001</div><div>; Highest order in the expansion of the constraint coupling matrix</div><div>lincs-order = 6</div><div>; Number of iterations in the final step of LINCS. 1 is fine for</div>
<div>; normal simulations, but use 2 to conserve energy in NVE runs.</div><div>; For energy minimization with constraints it should be 4 to 8.</div><div>lincs-iter = 2</div><div>; Lincs will write a warning to the stderr if in one step a bond</div>
<div>; rotates over more degrees than</div><div>lincs-warnangle = 30</div><div>; Convert harmonic bonds to morse potentials</div><div>morse = no</div><div><br></div><div>; ENERGY GROUP EXCLUSIONS</div>
<div>; Pairs of energy groups for which all non-bonded interactions are excluded</div><div>energygrp_excl =</div><div><br></div><div>; WALLS</div><div>; Number of walls, type, atom types, densities and box-z scale factor for Ewald</div>
<div>nwall = 0</div><div>wall_type = 9-3</div><div>wall_r_linpot = -1</div><div>wall_atomtype =</div><div> </div><div><div>; COM PULLING</div>
<div>; Pull type: no, umbrella, constraint or constant_force</div><div>pull = no</div><div><br></div><div>; NMR refinement stuff</div><div>; Distance restraints type: No, Simple or Ensemble</div><div>disre = No</div>
<div>; Force weighting of pairs in one distance restraint: Conservative or Equal</div><div>disre-weighting = Conservative</div><div>; Use sqrt of the time averaged times the instantaneous violation</div><div>disre-mixed = no</div>
<div>disre-fc = 1000</div><div>disre-tau = 0</div><div>; Output frequency for pair distances to energy file</div><div>nstdisreout = 100</div><div>; Orientation restraints: No or Yes</div>
<div>orire = no</div><div>; Orientation restraints force constant and tau for time averaging</div><div>orire-fc = 0</div><div>orire-tau = 0</div><div>orire-fitgrp =</div>
<div>; Output frequency for trace(SD) and S to energy file</div><div>nstorireout = 100</div><div>; Dihedral angle restraints: No or Yes</div><div>dihre = no</div><div>dihre-fc = 1000</div>
<div><br></div><div>; Free energy control stuff</div><div>free-energy = no</div><div>init-lambda = 0</div><div>delta-lambda = 0</div><div>sc-alpha = 0</div><div>sc-power = 0</div>
<div>sc-sigma = 0.3</div><div>couple-moltype =</div><div>couple-lambda0 = vdw-q</div><div>couple-lambda1 = vdw-q</div><div>couple-intramol = no</div><div><br></div><div>
; Non-equilibrium MD stuff</div><div>acc-grps =</div><div>accelerate =</div><div>freezegrps =</div><div>freezedim =</div><div>cos-acceleration = 0</div><div>
deform =</div><div><br></div><div>; Electric fields</div><div>; Format is number of terms (int) and for all terms an amplitude (real)</div><div>; and a phase angle (real)</div><div>E-x =</div>
<div>E-xt =</div><div>E-y =</div><div>E-yt =</div><div>E-z =</div><div>E-zt =</div><div> </div>
</div></div><div> </div></div></div><div><br><div class="gmail_quote">On Wed, Apr 8, 2009 at 1:00 PM, Joe Joe <span dir="ltr"><<a href="mailto:ilchorny@gmail.com">ilchorny@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br><br><div class="gmail_quote"><div class="im">On Wed, Apr 8, 2009 at 11:31 AM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br><br><div class="gmail_quote"><div>On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe <span dir="ltr"><<a href="mailto:ilchorny@gmail.com" target="_blank">ilchorny@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
HI Chris,<br><br><div class="gmail_quote"><div>On Tue, Apr 7, 2009 at 9:31 PM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
Hi Ilya,<br>
<br>
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.<br>
<br>
coulombtype = PME<br>
rcoulomb-switch = .9<br>
rcoulomb = 1.0</blockquote><div><br></div></div><div>I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case of PME but I will give it a try.</div></div></blockquote></div><div><br>It is indeed supported and does work correctly. But you have to set coulombtype PME-Switch. mdp options says:<br>
"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.
"<br> <br>Roland</div></div></blockquote><div><br></div></div><div>Yes, my point was that when electrostatics = PME then Gromacs ignores the rcoulomb-switch parameter.</div><div><div></div><div class="h5"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="gmail_quote"><div><br><br></div><div><div></div><div><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex"><div class="gmail_quote">
<div></div><div><div></div><div>
<div><br></div><blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex"><br>
<br>
Chris<br>
<br>
-- original message --<br>
<br>
Hi<br>
I am having some pressure coupling issues. I have a fairly large<br>
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I<br>
run NVE it conserves energy with appropriate parameter settings. If I run<br>
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello<br>
Rahman), the system just continuously expands. My parameters are as follows.<br>
Any ideas?<br>
<br>
Best,<br>
<br>
Ilya<br>
<br>
;<br>
; File 'mdout.mdp' was generated<br>
; By user: relly (508)<br>
; On host: <a href="http://master.simprota.com" target="_blank">master.simprota.com</a><br>
; At date: Fri Mar 6 20:17:33 2009<br>
;<br>
<br>
; VARIOUS PREPROCESSING OPTIONS<br>
; Preprocessor information: use cpp syntax.<br>
; e.g.: -I/home/joe/doe -I/home/mary/hoe<br>
include =<br>
; e.g.: -DI_Want_Cookies -DMe_Too<br>
define =<br>
<br>
; RUN CONTROL PARAMETERS<br>
integrator = md<br>
; Start time and timestep in ps<br>
tinit = 0<br>
dt = 0.004<br>
;nsteps = 250000<br>
nsteps = 2500000<br>
; For exact run continuation or redoing part of a run<br>
; Part index is updated automatically on checkpointing (keeps files<br>
separate)<br>
simulation_part = 1<br>
init_step = 0<br>
; mode for center of mass motion removal<br>
comm_mode = linear<br>
; number of steps for center of mass motion removal<br>
nstcomm = 1<br>
; group(s) for center of mass motion removal<br>
comm_grps = system<br>
<br>
; OUTPUT CONTROL OPTIONS<br>
; Output frequency for coords (x), velocities (v) and forces (f)<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
<br>
; Output frequency for energies to log file and energy file<br>
nstlog = 10<br>
nstenergy = 10<br>
; Output frequency and precision for xtc file<br>
nstxtcout = 250<br>
xtc-precision = 1000<br>
; This selects the subset of atoms for the xtc file. You can<br>
; select multiple groups. By default all atoms will be written.<br>
xtc-grps = protein<br>
; Selection of energy groups<br>
energygrps =<br>
<br>
; NEIGHBORSEARCHING PARAMETERS<br>
; nblist update frequency<br>
nstlist = 5<br>
; ns algorithm (simple or grid)<br>
ns_type = grid<br>
; Periodic boundary conditions: xyz, no, xy<br>
pbc = xyz<br>
periodic_molecules = no<br>
; nblist cut-off<br>
rlist = 1.0<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
; Method for doing electrostatics<br>
coulombtype = PME<br>
rcoulomb-switch = .9<br>
rcoulomb = 1.0<br>
; Relative dielectric constant for the medium and the reaction field<br>
epsilon-r = 80<br>
epsilon_rf = 1<br>
; Method for doing Van der Waals<br>
vdw-type = Switch<br>
; cut-off lengths<br>
rvdw-switch = .9<br>
rvdw = 1.0<br>
; Apply long range dispersion corrections for Energy and Pressure<br>
DispCorr = EnerPres<br>
; Extension of the potential lookup tables beyond the cut-off<br>
table-extension = 1<br>
; Seperate tables between energy group pairs<br>
energygrp_table =<br>
; Spacing for the PME/PPPM FFT grid<br>
fourierspacing = 0.12<br>
; FFT grid size, when a value is 0 fourierspacing will be used<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
; EWALD/PME/PPPM parameters<br>
pme_order = 4<br>
ewald_rtol = 1.e-05<br>
ewald_geometry = 3d<br>
epsilon_surface = 0<br>
optimize_fft = no<br>
; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>
; Temperature coupling<br>
Tcoupl = V-rescale<br>
; Groups to couple separately<br>
tc-grps = System<br>
; Time constant (ps) and reference temperature (K)<br>
tau_t = 0.1<br>
ref_t = 298.0<br>
; Pressure coupling<br>
Pcoupl = Berendsen<br>
Pcoupltype = Isotropic<br>
; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>
tau_p = 10<br>
compressibility = 4.5e-5<br>
ref_p = 1.01325<br>
; Scaling of reference coordinates, No, All or COM<br>
refcoord_scaling = No<br>
; Random seed for Andersen thermostat<br>
andersen_seed = 815131<br>
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