<div>Please see the following pr.mdp and full.mdp</div>
<div>pr.mdp</div>
<div> </div>
<div><font size="2">
<p>cpp = /usr/bin/cpp</p>
<p>define = -DPOSRES</p>
<p>constraints = all-bonds</p>
<p>integrator = md</p>
<p>dt = 0.002 ; ps !</p>
<p>nsteps = 50000 ; total 100 ps.</p>
<p>nstcomm = 1</p>
<p>nstxout = 500</p>
<p>nstvout = 1000</p>
<p>nstfout = 0</p>
<p>nstlog = 10</p>
<p>nstenergy = 10</p>
<p>nstlist = 10</p>
<p>ns_type = grid</p>
<p>rlist = 1.0</p>
<p>rcoulomb = 1.0</p>
<p>rvdw = 1.0</p>
<p>; Berendsen temperature coupling is on in two groups</p>
<p>Tcoupl = berendsen</p>
<p>tc-grps = Protein Non-protein </p>
<p>tau_t = 0.1 0.1 </p>
<p>ref_t = 500 500 </p>
<p>; Energy monitoring</p>
<p>energygrps = Protein Non-protein</p>
<p>; Pressure coupling is not on</p>
<p>Pcoupl = no</p>
<p>tau_p = 0.5</p>
<p>compressibility = 4.5e-5</p>
<p>ref_p = 1.0</p>
<p>; Generate velocites is on at 500 K.</p>
<p>gen_vel = yes</p>
<p>gen_temp = 500.0</p>
<p>gen_seed = 173529</p>
<p>full.mdp</p><font size="2">
<p>cpp = /usr/bin/cpp</p>
<p>constraints = all-bonds</p>
<p>integrator = md</p>
<p>dt = 0.002 ; ps !</p>
<p>nsteps = 50000000 ; total 100000 ps.</p>
<p>nstcomm = 1</p>
<p>nstxout = 5000</p>
<p>nstvout = 40000</p>
<p>nstfout = 0</p>
<p>nstlog = 100</p>
<p>nstenergy = 100</p>
<p>nstlist = 10</p>
<p>ns_type = grid</p>
<p>rlist = 1.0</p>
<p>rcoulomb = 1.0</p>
<p>rvdw = 1.0</p>
<p>; Berendsen temperature coupling is on in two groups</p>
<p>Tcoupl = berendsen</p>
<p>tc-grps = Protein Non-protein</p>
<p>tau_t = 0.1 0.1 </p>
<p>ref_t = 500 500</p>
<p>; Energy monitoring</p>
<p>energygrps = Protein Non-protein</p>
<p>; Isotropic pressure coupling is now on</p>
<p>Pcoupl = berendsen</p>
<p>Pcoupltype = isotropic</p>
<p>tau_p = 0.5</p>
<p>compressibility = 4.5e-5</p>
<p>ref_p = 1.0</p>
<p>; Generate velocites is off at 500 K.</p>
<p>gen_vel = no</p>
<p>gen_temp = 500.0</p>
<p>gen_seed = 173529</p>
<p>Please tell me why protein shows unfolding in very first frame. </p>
<p>msnayeem</p>
<p> </p></font>
<p> </p></font><br><br> </div>
<div><span class="gmail_quote">On 4/7/10, <b class="gmail_sendername">Mark Abraham</b> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span>On 7/04/2010 9:08 PM, shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear users<br>Please let me know some basic question. I am sorry if I am asking a<br>silly question.<br>a) While simulating a protein thermal unfolding at high temperature say<br>
500K should I run position restraint dynamics at 500k or at 298K. I am<br>doing 100ps position restraint dynamics at 500k. Am I right in doing so.<br></blockquote><br></span>The usual purpose of position restrained MD is to allow the system to achieve close to the ensemble desired for the start of the simulation without perturbing the initial structure.<span><br>
<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">b) While using Berendsen thermostat, how to select a value of tau_t and<br>how does it affects simulation output. The same question for NoseHoover<br>
thermostat.<br></blockquote><br></span>Start by reading the GROMACS manual sections.<span><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">c) After completing the 100ns simulation when I view the .xtc file in<br>VMD I find that alpha helix of the protein is unfolded in very first<br>
frame collected at 10ps interval and reduced by trjconv at 50ps<br>interval. Is it possible. If not then where I am wrong.<br>I did Steepest descent minimization, then 100ps position restraint<br>Dynamics at 500K and then 100ns full dynamics at 500k.<br>
</blockquote><br></span>10ps would be very fast for a lengthy helix to unfold, however you've deliberately taken your force field out of the zone where it was parameterized, so we can't really infer anything about its behaviour. You could also have a broken model physics in your .mdp file, but we can't know about that.<br>
<br>The real lesson here is not to do a lengthy simulation without looking at the early and ongoing results.<br><br>Mark<br><span>-- <br>gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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