I tried .1, and 10 ps tau_p values. I guess I can try smaller values.<div><br><div><br></div><div><br><div class="gmail_quote">On Wed, Apr 8, 2009 at 10:44 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Joe Joe wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Chris,<br>
<br>
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. <br>
</blockquote>
<br></div>
In addition to what Chris has been saying about constraints, consider your pressure coupling settings themselves<div class="im"><br>
<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>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks,<br>
<br>
Ilya<div class="im"><br>
<br>
<br>
On Wed, Apr 8, 2009 at 8:37 AM, <<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a> <mailto:<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>>> wrote:<br>
<br>
Hi Ilya,<br>
<br>
If you did include the entire mdp file then you have a time step of<br>
4 fs and no constraints (other than water). For a timestep of 2 fs,<br>
you should constrain all-bonds (or some would say at least h-bonds)<br>
and for 4 fs then you should also constrain angles involving<br>
hydrogens (need a new .itp file for this).<br>
<br>
Can you try with a 1 fs timestep and see how it goes? Still, I am<br>
surprised that everything works out at NVT, but this is certainly<br>
worth the test.<br>
<br>
Do you have other systems running fine with these mdp options in NVT?<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
HI Chris,<br>
<br>
On Tue, Apr 7, 2009 at 9:31 PM, <chris.neale at <a href="http://utoronto.ca" target="_blank">utoronto.ca</a><br></div><div><div></div><div class="h5">
<<a href="http://utoronto.ca" target="_blank">http://utoronto.ca</a>>> wrote:<br>
<br>
Hi Ilya,<br>
<br>
First thing that comes to mind is that it is strange to couple a<br>
coulombic<br>
switching function with PME. While this could possibly be done<br>
correctly, I<br>
doubt that it is in fact done in the way that you expect (i.e.<br>
correctly) in<br>
gromacs. In fact, I think that grompp/mdrun should probably<br>
throw an error<br>
here -- unless it is actually handled in the proper way, and a<br>
developer<br>
could help you here to figure out if you are indeed getting what<br>
you desire.<br>
<br>
coulombtype = PME<br>
rcoulomb-switch = .9<br>
rcoulomb = 1.0<br>
<br>
<br>
<br>
I am pretty sure gromacs ignores the rcoulomb-switch parameter in<br>
the case<br>
of PME but I will give it a try.<br>
<br>
<br>
<br>
However, it is not clear to me that this should cause a system to<br>
"continuously expand".<br>
<br>
Still, you do not give very good information about what you mean by<br>
"continuously expand". Can you please provide some information<br>
on that? e.g.<br>
amount of time and total volume change.<br>
<br>
<br>
<br>
My box density goes from ~1.0 to .5 in 5 ps with a compressibility<br>
of 5E-05.<br>
It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06.<br>
In both<br>
case the slope of density(t) is negative and never levels off.<br>
<br>
<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 <<br>
1000). If I<br>
run NVE it conserves energy with appropriate parameter settings.<br>
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<br>
follows.<br>
Any ideas?<br>
<br>
Best,<br>
<br>
Ilya<br>
<br>
;<br>
; File 'mdout.mdp' was generated<br>
; By user: relly (508)<br></div></div>
; On host: <a href="http://master.simprota.com" target="_blank">master.simprota.com</a> <<a href="http://master.simprota.com" target="_blank">http://master.simprota.com</a>><div><div></div><div class="h5">
<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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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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