Thank u for reply. I did energy minimization and equilibration step. It converged in 696 steps which is shown below.<div><br><div><div>Step= 692, Dmax= 9.2e-03 nm, Epot= -7.12587e+05 Fmax= 7.62150e+03, atom= 2099</div><div>
Step= 693, Dmax= 1.1e-02 nm, Epot= -7.12588e+05 Fmax= 9.72038e+03, atom= 2099</div><div>Step= 695, Dmax= 6.6e-03 nm, Epot= -7.12670e+05 Fmax= 9.39830e+02, atom= 2099</div><div><br></div><div>writing lowest energy coordinates.</div>
<div><br></div><div>Steepest Descents converged to Fmax < 1000 in 696 steps</div><div>Potential Energy = -7.1266969e+05</div><div>Maximum force = 9.3982965e+02 on atom 2099</div><div>Norm of force = 2.1967674e+01</div>
<div><br></div><div><br></div><div># md.mdp file</div><div><br></div><div><div>title = protein</div><div>cpp = /lib/cpp ; location of cpp on SGI</div><div>constraints = all-bonds</div><div>integrator = md</div><div>dt = 0.002 ; ps !</div>
<div>nsteps = 1000000 ; total 50 ps.</div><div>nstcomm = 1</div><div>nstxout = 500 ; output coordinates every 1.0 ps</div><div>nstvout = 0</div><div>nstfout = 0</div><div>nstlist = 10</div><div>ns_type = grid</div><div>rlist = 0.9</div>
<div>coulombtype = PME</div><div>rcoulomb = 0.9</div><div>rvdw = 1.0</div><div>fourierspacing = 0.12</div><div>fourier_nx = 0</div><div>fourier_ny = 0</div><div>fourier_nz = 0</div><div>pme_order = 6</div><div>ewald_rtol = 1e-5</div>
<div>optimize_fft = yes</div><div>; Berendsen temperature coupling is on in four groups</div><div>Tcoupl = berendsen</div><div>tau_t = 0.1 0.1 0.1 0.1 0.1</div><div>tc-grps = protein ZN IMP sol NA+</div><div>ref_t = 300 300 300 300 300</div>
<div>; Pressure coupling is on</div><div>Pcoupl = berendsen</div><div>pcoupltype = isotropic</div><div>tau_p = 0.5</div><div>compressibility = 4.5e-5</div><div>ref_p = 1.0</div><div>; Generate velocites is on at 300 K.</div>
<div>gen_vel = yes</div><div>gen_temp = 300.0</div><div>gen_seed = 173529</div></div><div><br></div><div># pr.mdp file</div><div><br></div><div><div>title = protein</div><div>cpp = /lib/cpp ; location of cpp on SGI</div><div>
define = -DPOSRES</div><div>constraints = all-bonds</div><div>integrator = md</div><div>dt = 0.002 ; ps !</div><div>nsteps = 50000 ; total 20.0 ps.</div><div>nstcomm = 1</div><div>nstxout = 250 ; output coordinates every 0.5 ps</div>
<div>nstvout = 1000 ; output velocities every 2.0 ps</div><div>nstfout = 0</div><div>nstlog = 10</div><div>nstenergy = 10</div><div>nstlist = 10</div><div>ns_type = grid</div><div>rlist = 0.9</div><div>coulombtype = PME</div>
<div>rcoulomb = 0.9</div><div>rvdw = 1.0</div><div>fourierspacing = 0.12</div><div>fourier_nx = 0</div><div>fourier_ny = 0</div><div>fourier_nz = 0</div><div>pme_order = 6</div><div>ewald_rtol = 1e-5</div><div>optimize_fft = yes</div>
<div>; Berendsen temperature coupling is on in four groups</div><div>Tcoupl = V-rescale</div><div>tau_t = 0.1 0.1 0.1 0.1 0.1</div><div>tc_grps = protein ZN sol IMP NA+</div><div>ref_t = 300 300 300 300 300</div><div>; Pressure coupling is on</div>
<div>Pcoupl = no</div><div>pcoupltype = isotropic</div><div>tau_p = 0.5</div><div>compressibility = 4.5e-5</div><div>ref_p = 1.0</div><div>; Generate velocites is on at 300 K.</div><div>gen_vel = yes</div><div>gen_temp = 300.0</div>
<div>gen_seed = 173529</div></div><div><br></div><div>#em.mdp file</div><div><br></div><div><div>title = protein</div><div>cpp = /lib/cpp ; location of cpp on SGI</div><div>define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]</div>
<div>constraints = none</div><div>integrator = steep</div><div>dt = 0.002 ; ps !</div><div>nsteps = 2000</div><div>nstlist = 10</div><div>ns_type = grid</div><div>rlist = 0.9</div><div>coulombtype = PME ; Use particle-mesh ewald</div>
<div>rcoulomb = 0.9</div><div>rvdw = 1.0</div><div>fourierspacing = 0.12</div><div>fourier_nx = 0</div><div>fourier_ny = 0</div><div>fourier_nz = 0</div><div>pme_order = 4</div><div>ewald_rtol = 1e-5</div><div>optimize_fft = yes</div>
<div>;</div><div>; Energy minimizing stuff</div><div>;</div><div>emtol = 1000.0</div><div>emstep = 0.01</div></div><div><br></div><div>I need further help to trouble shoot this problem.</div><div><br></div><div><br></div>
<div><br></div><div><br><div class="gmail_quote">On Sat, Dec 3, 2011 at 10:46 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>
pragna lakshmi wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
I am trying to run protein-ligand complex simulation. At the final MD run step it is showing the following error. Can anybody tell me the solution for this error?<br>
<br>
</blockquote>
<br>
</div><a href="http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors#LINCS.<u></u>2fSETTLE.2fSHAKE_warnings</a><br>
<br>
There are hundreds of threads in the archive with the same issue and several possible solutions. Please consult the link above (and referenced pages), as well as other posts.<br>
<br>
If you need further help diagnosing the problem, please post a complete .mdp file, as well as a description of prior minimization and equilibration.<br>
<br>
-Justin<br>
<br>
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Virginia Tech<br>
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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.<u></u>vt.edu/Pages/Personal/justin</a><br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">T.Pragna Lakshmi,</span></div>
<div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Junior Scientist,</span></div><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt"><span style="font-family:"Times New Roman","serif";font-size:12pt">Vision Research Center,</span></span></div>
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