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On 3/12/2011 5:15 PM, pragna lakshmi wrote:
<blockquote
cite="mid:CAD6uh5tBO8wuvuUA9g+fjiV52BgS8FabOpq75yq-gcaDRy8HQQ@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
Such a conclusion would be premature, given your inappropriate use
of thermostats and the information in the URL Justin provided...<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAD6uh5tBO8wuvuUA9g+fjiV52BgS8FabOpq75yq-gcaDRy8HQQ@mail.gmail.com"
type="cite">
<br>
<div class="gmail_quote">On Sat, Dec 3, 2011 at 11:19 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a>
| (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><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>
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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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