I understood that the system has large velocities. Since simulation has been stopped at Step 226040, time 452.08 (ps) can i conclude that error is because of any invalid parameters in topology file generated by server for ligand.<br>
<br><div class="gmail_quote">On Sat, Dec 3, 2011 at 11:19 AM, 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 bgcolor="#FFFFFF" text="#000000"><div class="im">
On 3/12/2011 4:42 PM, pragna lakshmi wrote:
</div><div class="im"><blockquote type="cite">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>
</div>
</blockquote>
<br></div><div class="im">
The atom that has the greatest force after EM is the same one for
which LINCS warnings arise later. That's worth paying attention to.
Read the advice about diagnosing unstable systems on the link Justin
gave you last time.<br>
<br>
</div><blockquote type="cite">
<div>
<div>
<div><br>
</div><div><div class="h5">
<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>
</div></div></div>
</div>
</blockquote>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Thermostats" target="_blank">http://www.gromacs.org/Documentation/Terminology/Thermostats</a><div class="im"><br>
<br>
<blockquote type="cite">
<div>
<div>
<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>
</div>
</blockquote>
<br></div><div class="im">
It's probably not useful to re-generate velocities after the
position-restrained step.<br>
<br>
Mark<br>
<br>
</div><blockquote type="cite">
<div>
<div>
<div><br>
</div><div><div class="h5">
<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" target="_blank">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><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/Documentation/Errors#LINCS.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>
-- <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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-- <br>
<div style="line-height:normal"><span>T.Pragna
Lakshmi,</span></div>
<div style="line-height:normal"><span>Junior
Scientist,</span></div>
<div style="line-height:normal"><span><span>Vision
Research Center,</span></span></div>
<div style="line-height:normal"><span>Sankara
Netralaya,</span></div>
<div style="line-height:normal"><span>Chennai,</span></div>
<div style="line-height:normal"><span>India.</span></div>
<div style="line-height:normal"><span>Pin:
600006.</span></div>
<br>
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<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>
<div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Sankara Netralaya,</span></div><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Chennai,</span></div>
<div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">India.</span></div><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Pin: 600006.</span></div>
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