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On 19/12/2011 1:05 AM, aiswarya pawar wrote:
<blockquote
cite="mid:CAEa6cRB4zPo4xYXQ+L6RV9NgkxYK14eCC2uq0p8R67pqyFz_kg@mail.gmail.com"
type="cite">Hi users,
<div><br>
</div>
<div>I did energy minimization of a protein complex using the
following minimization mdp file.</div>
</blockquote>
<br>
See <a
href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a>
for general advice.<br>
<br>
<blockquote
cite="mid:CAEa6cRB4zPo4xYXQ+L6RV9NgkxYK14eCC2uq0p8R67pqyFz_kg@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
You are asking for trouble by generating velocities and doing
position restraints with P-R pressure coupling in one step. It might
work, but the workflow in the above link is safer.<br>
<br>
<blockquote
cite="mid:CAEa6cRB4zPo4xYXQ+L6RV9NgkxYK14eCC2uq0p8R67pqyFz_kg@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
Why are you re-generating non-equilibrium velocities after
equilibrating them?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEa6cRB4zPo4xYXQ+L6RV9NgkxYK14eCC2uq0p8R67pqyFz_kg@mail.gmail.com"
type="cite">
<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>
<br>
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<br>
</blockquote>
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