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.ne...@utoronto.ca
<mailto:chris.ne...@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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