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<p class="MsoNormal">Hi All,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I wish to simulate a protein in its crystal
form. The
crystal is a triclinic box with a C2 symmetry. <span style=""> </span>I
have built the unit cell, which has 4 copies of the
protein, and add some water on top of the ones in the pdb. Then
minimized and run positional restrained MD
followed by a non restrained MD. The system crashed after ~600ps
reporting of LINCS errors.<br>
</p>
<p class="MsoNormal"><br>
Now I
have minimized it before running; I have checked the topology and
could not
find any error; I have also tried to run it in shake and the
system crashed as
well; I also run the system in NVT without any success.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I guess this is a symptom to something like
pressure
problems, PBC issues or bad topology, but I could not find it. I
also looked
for an isolated water molecule which might have caused it, without
any success.
So I hope someone else can come with the bright idea I don’t have.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">The rate of water and protein is ~1 protein to
300 water
molecules, In addition I add NaCl to neutralise the system and
bring it to 0.1M
concentration. </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Also here is my mdp file:</p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">integrator<span style=""> </span><span
style=""> </span><span style=""> </span>=<span style="">
</span>md</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">dt<span style="">
</span><span style=""> </span><span style=""> </span>=<span
style="">
</span>0.002<span style=""> </span>; ps
!</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">nsteps<span style="">
</span><span style=""> </span><span style=""> </span>=<span
style="">
</span>2500000</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";"> </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; OPTIONS FOR BONDS</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Constrain control</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">constraints<span style=""> </span><span
style="">
</span>=<span style=""> </span>all-bonds</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Do not constrain
the start configuration</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">continuation<span style=""> </span>= yes</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Type of constraint
algorithm</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">constraint-algorithm<span style=""> </span>=<span
style=""> </span>lincs</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";"> </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; OUTPUT CONTROL
OPTIONS</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Output frequency
for coords (x), velocities (v) and forces (f)</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">nstxout<span style="">
</span>=<span style=""> </span>100000</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">nstvout<span style="">
</span><span style=""> </span><span style=""> </span>=<span
style="">
</span>100000</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">nstfout<span style="">
</span><span style=""> </span><span style=""> </span>=<span
style="">
</span>100000</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Output frequency
and precision for xtc file</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">nstxtcout<span style=""> </span><span
style=""> </span><span style=""> </span>=<span style="">
</span>2500</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">xtc-precision<span style=""> </span><span
style=""> </span><span style=""> </span>=<span style="">
</span>1000</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Energy monitoring</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">energygrps<span style=""> </span><span
style=""> </span><span style=""> </span>=<span style="">
</span>Protein</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">nstenergy<span style=""> </span><span style="">
</span>=<span style=""> </span>1000</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";"> </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; NEIGHBORSEARCHING
PARAMETERS</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; nblist update
frequency</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">nstlist<span style="">
</span><span style=""> </span><span style=""> </span>=<span
style="">
</span>5 </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; ns algorithm
(simple or grid)</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">ns-type<span style="">
</span><span style=""> </span><span style=""> </span>=<span
style="">
</span>Grid</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; nblist
cut-off<span style=""> </span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">rlist<span style="">
</span><span style=""> </span><span style=""> </span>=<span
style="">
</span>0.8</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";"> </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; OPTIONS FOR ELECTROSTATICS
AND VDW</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Method for doing
electrostatics</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">coulombtype<span style="">
</span>= Reaction-Field<span style=""> </span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">rcoulomb <span style=""> </span><span style="">
</span><span style=""> </span>= 1.4 </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">epsilon_rf<span style=""> </span><span style="">
</span> = 62<span style=""> </span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">vdw-type<span style="">
</span>= Cut-off</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; cut-off
lengths<span style="">
</span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">rvdw-switch<span style="">
</span>= 0</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">rvdw<span style="">
</span>= 1.4</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Apply long range
dispersion corrections for Energy and Pressure</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">DispCorr<span style="">
</span>= no</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";"> </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; OPTIONS FOR WEAK
COUPLING ALGORITHMS</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Temperature
coupling<span style=""> </span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">tcoupl<span style=""> </span><span style=""> </span>=
berendsen</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Groups to couple
separately, time constant (ps) and reference temperature (K)</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">tc-grps<span style="">
</span>= Protein<span style=""> </span>solvent<span style="">
</span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">tau-t<span style="">
</span>= 0.1<span style=""> </span><span style=""> </span>0.1
</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">ref-t<span style="">
</span>= 300<span style=""> </span><span style=""> </span>300<span
style=""> </span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Pressure coupling<span style=""> </span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">Pcoupl<span style="">
</span>= no</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">Pcoupltype<span style="">
</span>= isotropic</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Time constant
(ps), compressibility (1/bar) and reference P (bar)</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">tau_p<span style="">
</span>=<span style=""> </span>1.0<span style=""> </span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">compressibility<span style=""> </span><span
style=""> </span><span style=""> </span>=<span style="">
</span>4.5e-5<span style="">
</span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">ref_p<span style="">
</span><span style=""> </span><span style=""> </span>=<span
style="">
</span>1.0<span style=""> </span></span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Do not generate velocities</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">gen_vel<span style="">
</span>=<span style=""> </span>no</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";"> </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Center of mass
control</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">nstcomm<span style="">
</span>=<span style=""> </span>10000</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Periodic boundary
conditions </span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">pbc<span style="">
</span>=<span style=""> </span>xyz</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Mode for center of
mass motion removal</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">comm-mode<span style="">
</span>=<span style=""> </span>Linear</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">; Groups for center
of mass motion removal</span></p>
<p class="MsoNormal"><span style="font-family: "Courier
New";">comm-grps<span style="">
</span>=<span style=""> </span>system</span></p>
<p class="MsoNormal"> <br>
</p>
<p class="MsoNormal">Thanks in advance,<br>
Itamar.<br>
</p>
<pre class="moz-signature" cols="72">--
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a>
============================================</pre>
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