<br /><br /><span>On 20/12/11, <b class="name">aiswarya pawar </b> <aiswarya.pawar@gmail.com> wrote:</span><blockquote cite="mid:CAEa6cRDo8YGZmo2Ek+nJWotckWwPfQNN18uP9CCQ=uFKbCRy=w@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid #00F; padding-left: 13px; margin-left: 0;" type="cite"><div class="mimepart text html">i went through the mailing list, but i dont understand when i run the same protein on my computer it runs correctly without any LINCS warning. On the cluster with 64 processors the job runs but crashes in between and shows the LINCS warning. </div></blockquote><div><br /></div><div>That happens. Your different computers are running different versions of the calculation. Numerical artefacts do happen, especially if you use algorithms that are known to be unstable when not in equilibrium, like I said three days ago. Why have you repeated your question instead of trying my suggestion?</div><div><br /></div><blockquote cite="mid:CAEa6cRDo8YGZmo2Ek+nJWotckWwPfQNN18uP9CCQ=uFKbCRy=w@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid #00F; padding-left: 13px; margin-left: 0;" type="cite"><div class="mimepart text html">Please anyone tell me what could be the reason. Is anything wrong with my protein.</div></blockquote><div><br /></div><div>Something is very likely wrong with your system preparation. The links people have been giving you detail the advice on how to diagnose the problem or how to be more gentle. There's little else for me to say.</div><div><br /></div><div>Mark </div><blockquote cite="mid:CAEa6cRDo8YGZmo2Ek+nJWotckWwPfQNN18uP9CCQ=uFKbCRy=w@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid #00F; padding-left: 13px; margin-left: 0;" type="cite"><div class="mimepart text html"><br /><br /><br /><div class="gmail_quote">On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar <span dir="ltr"><<a href="mailto:aiswarya.pawar@gmail.com">aiswarya.pawar@gmail.com</a>></span> wrote:<br />
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi users,<div><br /></div><div>I did energy minimization of a protein complex using the following minimization mdp file.</div>
<div><br /></div><div><div>; Lines starting with ';' ARE COMMENTS</div><div>; Everything following ';' is also comment</div>
<div><br /></div><div>title<span style="white-space:pre-wrap"> </span>= Energy Minimization; Title of run</div><div><br /></div><div>; The following line tell the program the standard locations where to find certain files</div>
<div>cpp<span style="white-space:pre-wrap"> </span>= /lib/cpp; Preprocessor</div><div><br /></div><div><br /></div><div>; Define can be used to control processes</div>
<div>define = -DFLEXIBLE</div><div><br /></div><div>; Parameters describing what to do, when to stop and what to save</div><div>integrator= steep<span style="white-space:pre-wrap"> </span>; Algorithm (steep = steepest descent minimization)</div>
<div>emtol<span style="white-space:pre-wrap"> </span>= 1000.0 ; Stop minimization when the maximum force < 1.0 kJ/mol</div><div>emstep = 0.01</div>
<div>nsteps<span style="white-space:pre-wrap"> </span>= 5000<span style="white-space:pre-wrap"> </span>; Maximum number of (minimization) steps to perform</div><div>nstenergy= 10<span style="white-space:pre-wrap"> </span>; Write energies to disk every nstenergy steps</div>
<div>energygrps= Protein; Which energy group(s) to write to disk</div><div><br /></div><div>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions</div>
<div>nstlist<span style="white-space:pre-wrap"> </span>= 10<span style="white-space:pre-wrap"> </span>; Frequency to update the neighbor list and long range forces</div><div>ns_type<span style="white-space:pre-wrap"> </span>= grid ; Method to determine neighbor list (simple, grid)</div>
<div>rlist<span style="white-space:pre-wrap"> </span>= 1.0<span style="white-space:pre-wrap"> </span>; Cut-off for making neighbor list (short range forces)</div><div>coulombtype= PME ; Treatment of long range electrostatic interactions</div>
<div>rcoulomb= 1.0<span style="white-space:pre-wrap"> </span>; long range electrostatic cut-off</div><div>rvdw<span style="white-space:pre-wrap"> </span>= 1.4<span style="white-space:pre-wrap"> </span>; long range Van der Waals cut-off</div>
<div>constraints= none<span style="white-space:pre-wrap"> </span>; Bond types to replace by constraints</div><div>pbc<span style="white-space:pre-wrap"> </span> = xyz<span style="white-space:pre-wrap"> </span>; Periodic Boundary Conditions (yes/no)</div>
</div><div><br /></div><div><br /></div><div>and the pr.mdp =</div><div><br /></div><div><div><div>; VARIOUS PREPROCESSING OPTIONS</div><div>title = Position Restrained Molecular Dynamics</div><div>define = -DPOSRES</div>
<div><br /></div><div>constraints = all-bonds</div><div>integrator = md</div><div>dt = 0.001 ; ps !</div><div>nsteps = 25000 ; total 50 ps.</div><div>nstcomm = 10</div>
<div>nstxout = 500 ; collect data every 1 ps</div><div>nstxtcout = 500</div><div>nstvout = 0</div><div>nstfout = 0</div><div>nstlist = 10</div>
<div>ns_type = grid</div><div>rlist = 1.0</div><div>coulombtype = PME</div><div>rcoulomb = 1.0</div><div>vdwtype = cut-off</div><div>rvdw = 1.4</div>
<div>pme_order = 4</div><div>ewald_rtol = 1e-5</div><div>optimize_fft = yes</div><div>DispCorr = no</div><div>; Berendsen temperature coupling is on</div><div>Tcoupl = v-rescale</div>
<div>tau_t = 0.1 0.1</div><div>tc-grps = protein non-protein</div><div>ref_t = 300 300</div><div>; Pressure coupling is on</div><div>Pcoupl = parrinello-rahman</div>
<div>Pcoupltype = isotropic</div><div>tau_p = 1.0</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 = -1</div></div></div><div><br /></div><div>and md.mdp file =</div><div><br /></div><div><div>; VARIOUS PREPROCESSING OPTIONS</div>
<div>title = Position Restrained Molecular Dynamics</div><div><br /></div><div><br /></div><div>; RUN CONTROL PARAMETERS</div><div>constraints = all-bonds</div><div>integrator = md</div><div>dt = 0.002 ; 2fs !</div>
<div>nsteps = 2500000 ; total 5000 ps.</div><div>nstcomm = 10</div><div>nstxout = 500 ; collect data every 1 ps</div><div>nstxtcout = 0</div><div>nstvout = 0</div><div>nstfout = 0</div><div>nstlist = 10</div><div>ns_type = grid</div>
<div>rlist = 1.0</div><div>coulombtype = PME</div><div>rcoulomb = 1.0</div><div>vdwtype = cut-off</div><div>rvdw = 1.4</div><div>pme_order = 4</div><div>ewald_rtol = 1e-5</div><div>optimize_fft = yes</div><div>DispCorr = no</div>
<div>; Berendsen temperature coupling is on</div><div>Tcoupl = v-rescale</div><div>tau_t = 0.1 0.1</div><div>tc-grps = protein non-protein</div><div>ref_t = 300 300</div><div>; Pressure coupling is on</div><div>Pcoupl = parrinello-rahman</div>
<div>Pcoupltype = isotropic</div><div>tau_p = 1.0</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 = -1</div>
</div><div><br /></div><div><br /></div><div>The minimization step went well. but while doing the final mdrun am getting LINCS error. i read through the numerous mailing list on grimaces but still couldn't understand how would i fix this. am getting this error for all the 10 protein complex i did minimization for. Please help.</div>
<div><br /></div><div><br /></div><div>Thanks,</div><div>Aiswarya</div><div><br /></div>
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