<div dir="ltr">Well, the final average pressure is not correct:<div><br></div><div><div><span class="Apple-tab-span" style="white-space:pre"><b> </b></span><b><====== ############### ==></b></div><div><span class="Apple-tab-span" style="white-space:pre"><b> </b></span><b><==== A V E R A G E S ====></b></div>
<div><span class="Apple-tab-span" style="white-space:pre"><b> </b></span><b><== ############### ======></b></div><div><b><br></b></div><div><b> Energies (kJ/mol)</b></div><div><b> Buck.ham (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.</b></div>
<div><b> 1.60633e+06 -5.69243e+06 -3.45003e+06 -7.53612e+06 1.80719e+04</b></div><div><b> Total Energy Temperature Pressure (bar)</b></div><div><b> -7.51805e+06 3.62347e+02 1.11758e+04</b></div><div>
<b><br></b></div><div><b><br></b></div><div><b> Pressure (bar)</b></div><div><b> 1.21051e+04 -2.94017e-01 1.30456e+00</b></div><div><b> -2.94017e-01 9.03597e+03 -8.10850e-01</b></div><div><b> 1.30456e+00 -8.10850e-01 1.23863e+04</b></div>
<div><b><br></b></div><div><b><br></b></div><div><span class="Apple-tab-span" style="white-space:pre"><b> </b></span><b><====== ############################### ==></b></div><div><span class="Apple-tab-span" style="white-space:pre"><b> </b></span><b><==== R M S - F L U C T U A T I O N S ====></b></div>
<div><span class="Apple-tab-span" style="white-space:pre"><b> </b></span><b><== ############################### ======></b></div><div><b><br></b></div><div><b> Energies (kJ/mol)</b></div><div><b> Buck.ham (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.</b></div>
<div><b> 3.92376e+05 4.00326e+05 4.71365e+01 3.02978e+04 2.35039e+03</b></div><div><b> Total Energy Temperature Pressure (bar)</b></div><div><b> 3.01091e+04 4.71259e+01 1.71117e+05</b></div><div>
<b><br></b></div><div><b><br></b></div><div><b> Pressure (bar)</b></div><div><b> 1.82323e+05 4.91513e+02 3.07107e+02</b></div><div><b> 4.91513e+02 2.02402e+05 3.13857e+02</b></div><div><b> 3.07107e+02 3.13857e+02 1.30179e+05</b></div>
<div><b><br></b></div><div><b>Also the fluctuation is very large. I think 200ps is long enough. But still I cannot find the equilibrium.</b></div><div><b>I do not know whether the parameters are wrong or I ran the anisotropic pressure coupling wrong. Is </b><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Parrinello-Rahman pressure coupling sensitive to the initial pressure? I mean if the initial pressure ( in order of GPa), object pressure is 1 bar ( 1e5 Pa). </span></div>
<div><b><br></b></div>Thanks,<br>Shuangxing Dai<br>
<br><br><div class="gmail_quote">On Mon, Jun 14, 2010 at 8:50 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Message: 3<br>
Date: Mon, 14 Jun 2010 19:18:14 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] anisotropic pressure coupling<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4C16B8B6.4010005@vt.edu">4C16B8B6.4010005@vt.edu</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<br>
<br>
Shuangxing Dai wrote:<br>
> Hi all:<br>
> I was using Parrinello-Rahman for pressure coupling and here is the<br>
> mdp file:<br>
><br>
> ; RUN CONTROL PARAMETERS =<br>
> integrator = sd<br>
> ; start time and timestep in ps =<br>
> tinit = 0<br>
> dt = 0.001<br>
> nsteps = 200000<br>
> ; number of steps for center of mass motion removal =<br>
> nstcomm = 100<br>
> ; NEIGHBORSEARCHING PARAMETERS =<br>
> ; nblist update frequency =<br>
> nstlist = 50<br>
> ; ns algorithm (simple or grid) =<br>
> ns_type = grid<br>
><br>
> ;OPTIONS FOR PRESSURE COUPLING<br>
> Pcoupl = Parrinello-Rahman<br>
> pcoupltype = anisotropic<br>
> tau_p = 1<br>
> compressibility = 2.1645e-09 2.1645e-09 2.7322e-09 0 0 0<br>
> ref_p = 1 1 1 0 0 0<br>
> ;OPTIONS FOR TEMPERATURE COUPLING<br>
> tc_grps = system<br>
> tau_t = 0.1<br>
> ref_t = 300<br>
> ; OPTIONS FOR BONDS =<br>
> constraints = hbonds<br>
> ; Type of constraint algorithm =<br>
> constraint-algorithm = Lincs<br>
> ; Do not constrain the start configuration =<br>
> unconstrained-start = no<br>
> ; Relative tolerance of shake =<br>
> shake-tol = 0.0001<br>
> ; Highest order in the expansion of the constraint coupling matrix =<br>
> lincs-order = 12<br>
> ; Lincs will write a warning to the stderr if in one step a bond =<br>
> ; rotates over more degrees than =<br>
> lincs-warnangle = 30<br>
> ; Periodic boundary conditions: xyz, no, xy<br>
> pbc = xyz<br>
> periodic_molecules = no<br>
> ; nblist cut-off<br>
> rlist = 1<br>
><br>
> ; OPTIONS FOR ELECTROSTATICS AND VDW<br>
> ; Method for doing electrostatics<br>
> coulombtype = PME<br>
> rcoulomb = 1<br>
> ; Method for doing Van der Waals<br>
> vdw-type = Cut-off<br>
> ; cut-off lengths<br>
> rvdw = 1<br>
><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 = 6<br>
> ewald_rtol = 1e-4<br>
> ewald_geometry = 3d<br>
> epsilon_surface = 0<br>
> optimize_fft = no<br>
><br>
> It seems that the temperature coupling is fast and fluctuation is less<br>
> that 1%. But the pressure coupling fails. The pressure fluctuates from<br>
> +1e3 bar to -1e3 bar. Anyone can help?<br>
><br>
<br>
I don't call that failure. Depending on the size of your system, you can<br>
probably expect very wide fluctuations in the pressure. Is the average correct?<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Pressure" target="_blank">http://www.gromacs.org/Documentation/Terminology/Pressure</a><br>
<br>
-Justin<br>
<br>
><br>
> Thanks,<br>
> Shuangxing Dai<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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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