the log file just lists all the parameters of the simulation, following is a part of it<div><br></div><div><div>parameters of the run:</div><div> integrator = md</div><div> nsteps = 4000</div><div>
init_step = 0</div><div> ns_type = Grid</div><div> nstlist = 10</div><div> ndelta = 2</div><div> nstcomm = 0</div><div> comm_mode = Linear</div>
<div> nstlog = 1000</div><div> nstxout = 1000</div><div> nstvout = 0</div><div> nstfout = 500</div><div> nstenergy = 10</div><div> nstxtcout = 0</div>
<div> init_t = 0</div><div> delta_t = 0.002</div><div> xtcprec = 1000</div><div> nkx = 0</div><div> nky = 0</div><div> nkz = 0</div>
<div> pme_order = 4</div><div> ewald_rtol = 1e-05</div><div> ewald_geometry = 0</div><div> epsilon_surface = 0</div><div> optimize_fft = FALSE</div><div> ePBC = xy</div>
<div> bPeriodicMols = FALSE</div><div> bContinuation = FALSE</div><div> bShakeSOR = FALSE</div><div> etc = No</div><div> epc = No</div><div> epctype = Isotropic</div>
<div> tau_p = 1</div><div> ref_p (3x3):</div><div> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div>
<div> compress (3x3):</div><div> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div>
<div> refcoord_scaling = No</div><div> posres_com (3):</div><div> posres_com[0]= 0.00000e+00</div><div> posres_com[1]= 0.00000e+00</div><div> posres_com[2]= 0.00000e+00</div><div> posres_comB (3):</div>
<div> posres_comB[0]= 0.00000e+00</div><div> posres_comB[1]= 0.00000e+00</div><div> posres_comB[2]= 0.00000e+00</div><div> andersen_seed = 815131</div><div> rlist = 1.3</div><div> rtpi = 0.05</div>
<div> coulombtype = Reaction-Field-zero</div><div> rcoulomb_switch = 0</div><div> rcoulomb = 1</div><div> vdwtype = Shift</div><div> rvdw_switch = 0.9</div><div> rvdw = 1</div>
<div> epsilon_r = 1</div><div> epsilon_rf = inf</div><div> tabext = 1</div><div> implicit_solvent = No</div><div> gb_algorithm = Still</div><div> gb_epsilon_solvent = 80</div>
<div> nstgbradii = 1</div><div> rgbradii = 2</div><div> gb_saltconc = 0</div><div> gb_obc_alpha = 1</div><div> gb_obc_beta = 0.8</div><div> gb_obc_gamma = 4.85</div>
<div> sa_surface_tension = 2.092</div><div> DispCorr = No</div><div> free_energy = no</div><div> init_lambda = 0</div><div> sc_alpha = 0</div><div> sc_power = 0</div>
<div> sc_sigma = 0.3</div><div> delta_lambda = 0</div><div> nwall = 0</div><div> wall_type = 9-3</div><div> wall_atomtype[0] = -1</div><div> wall_atomtype[1] = -1</div>
<div> wall_density[0] = 0</div><div> wall_density[1] = 0</div><div> wall_ewald_zfac = 3</div><div> pull = no</div><div> disre = No</div><div> disre_weighting = Conservative</div>
<div> disre_mixed = FALSE</div><div> dr_fc = 1000</div><div> dr_tau = 0</div><div> nstdisreout = 100</div><div> orires_fc = 0</div><div> orires_tau = 0</div>
<div> nstorireout = 100</div><div> dihre-fc = 1000</div><div> em_stepsize = 0.01</div><div> em_tol = 10</div><div> niter = 20</div><div> fc_stepsize = 0</div>
<div> nstcgsteep = 1000</div><div> nbfgscorr = 10</div><div> ConstAlg = Lincs</div><div> shake_tol = 0.0001</div><div> lincs_order = 4</div><div> lincs_warnangle = 30</div>
<div> lincs_iter = 2</div><div> bd_fric = 0</div><div> ld_seed = 1993</div><div> cos_accel = 0</div><div> deform (3x3):</div><div> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div>
<div> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}</div><div> userint1 = 0</div><div> userint2 = 0</div>
<div> userint3 = 0</div><div> userint4 = 0</div><div> userreal1 = 0</div><div> userreal2 = 0</div><div> userreal3 = 0</div><div> userreal4 = 0</div>
<div>grpopts:</div><div> nrdf: 3.92594e+06</div><div> ref_t: 0</div><div> tau_t: 0</div><div>anneal: No</div><div>ann_npoints: 0</div><div> acc:<span class="Apple-tab-span" style="white-space:pre"> </span> 0 0 0</div>
<div> nfreeze: N N N</div><div> energygrp_flags[ 0]: 0 0</div><div> energygrp_flags[ 1]: 0 0</div><div> efield-x:</div><div> n = 0</div><div> efield-xt:</div><div> n = 0</div>
<div> efield-y:</div><div> n = 0</div><div> efield-yt:</div><div> n = 0</div><div> efield-z:</div><div> n = 0</div><div> efield-zt:</div><div> n = 0</div><div> bQMMM = FALSE</div>
<div> QMconstraints = 0</div><div> QMMMscheme = 0</div><div> scalefactor = 1</div><div>qm_opts:</div><div> ngQM = 0</div><div><br></div><br><div class="gmail_quote">On Fri, Feb 19, 2010 at 3:46 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</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>
----- Original Message -----<br>
From: Amit Choubey <<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>><br>
</div><div class="im">Date: Saturday, February 20, 2010 10:25<br>
Subject: Re: [gmx-users] domain decomposition and load balancing<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<br>
</div><div class="im">> Hi Mark and Justin,<br>
> I am using a box of size (20nm)x(20nm)x(60nm)..system is open along z ie (60nm) side.><br>
> I tried using only two nodes, it gives the same error><br>
<br>
> There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 0.889862 nm> Change the number of nodes or mdrun option -rdd or -dds> Look in the log file for details on the domain decomposition<br>
<br>
</div>... so what does the log file say?<br>
<font color="#888888"><br>
Mark<br>
</font><div><div></div><div class="h5"><br>
> On Fri, Feb 19, 2010 at 3:16 PM, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>> wrote:<br>
<br>
> ----- Original Message -----<br>
><br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
><br>
Date: Saturday, February 20, 2010 10:13<br>
><br>
Subject: Re: [gmx-users] domain decomposition and load balancing<br>
><br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<br>
><br>
><br>
><br>
><br>
><br>
<br>
> > Amit Choubey wrote:<br>
><br>
> >Hi Mark,<br>
><br>
> ><br>
><br>
> >I am not using PME calculation.<br>
><br>
> ><br>
><br>
> >I was hoping mdrun will do the cell allocation itself.<br>
><br>
> ><br>
><br>
><br>
><br>
> It will, unless it can't, which is exactly your problem. <br>
><br>
> Mark's point stands, regardless of whether or not you're using<br>
><br>
> PME. DD requires certain minimum size requirements (which<br>
><br>
> are discussed in the manual and the Gromacs 4 paper), so you<br>
><br>
> have two choices:<br>
><br>
><br>
><br>
> 1. Read about the options mdrun is telling you about.<br>
><br>
> 2. Use fewer nodes so that the DD algorithm can construct<br>
><br>
> reasonably-sized domains.<br>
<br>
><br>
<br>
> 3. Use a larger simulation system so the minimum cell size is larger w.r.t. the cutoffs<br>
><br>
4. (If reasonable) Don't use pbc=xy<br>
<br>
><br>
><br>
Mark<br>
><br>
--<br>
><br>
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<br>
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><br>
<br>
</div></div>> --<br>
<div class="im">> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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</div>--<br>
<div><div></div><div class="h5">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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</div></div></blockquote></div><br></div>