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 class="Apple-tab-span" style="white-space:pre"> </span>= Energy Minimization<span class="Apple-tab-span" style="white-space:pre"> </span>; 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 class="Apple-tab-span" style="white-space:pre"> </span>= /lib/cpp<span class="Apple-tab-span" style="white-space:pre"> </span>; 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<span class="Apple-tab-span" style="white-space:pre"> </span>= steep<span class="Apple-tab-span" style="white-space:pre"> </span>; Algorithm (steep = steepest descent minimization)</div>
<div>emtol<span class="Apple-tab-span" style="white-space:pre"> </span>= 1000.0 <span class="Apple-tab-span" style="white-space:pre"> </span>; Stop minimization when the maximum force < 1.0 kJ/mol</div><div>emstep = 0.01</div>
<div>nsteps<span class="Apple-tab-span" style="white-space:pre"> </span>= 5000<span class="Apple-tab-span" style="white-space:pre"> </span>; Maximum number of (minimization) steps to perform</div><div>nstenergy<span class="Apple-tab-span" style="white-space:pre"> </span>= 10<span class="Apple-tab-span" style="white-space:pre"> </span>; Write energies to disk every nstenergy steps</div>
<div>energygrps<span class="Apple-tab-span" style="white-space:pre"> </span>= Protein<span class="Apple-tab-span" style="white-space:pre"> </span>; 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 class="Apple-tab-span" style="white-space:pre"> </span>= 10<span class="Apple-tab-span" style="white-space:pre"> </span>; Frequency to update the neighbor list and long range forces</div><div>ns_type<span class="Apple-tab-span" style="white-space:pre"> </span>= grid <span class="Apple-tab-span" style="white-space:pre"> </span>; Method to determine neighbor list (simple, grid)</div>
<div>rlist<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.0<span class="Apple-tab-span" style="white-space:pre"> </span>; Cut-off for making neighbor list (short range forces)</div><div>coulombtype<span class="Apple-tab-span" style="white-space:pre"> </span>= PME <span class="Apple-tab-span" style="white-space:pre"> </span>; Treatment of long range electrostatic interactions</div>
<div>rcoulomb<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.0<span class="Apple-tab-span" style="white-space:pre"> </span>; long range electrostatic cut-off</div><div>rvdw<span class="Apple-tab-span" style="white-space:pre"> </span>= 1.4<span class="Apple-tab-span" style="white-space:pre"> </span>; long range Van der Waals cut-off</div>
<div>constraints<span class="Apple-tab-span" style="white-space:pre"> </span>= none<span class="Apple-tab-span" style="white-space:pre"> </span>; Bond types to replace by constraints</div><div>pbc<span class="Apple-tab-span" style="white-space:pre"> </span> = xyz<span class="Apple-tab-span" style="white-space:pre"> </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>