Reply inline...<br><br><div class="gmail_quote">On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I have a system of 3600 LJ particles in a plane (using freeze-dimension option in z). I am running npt runs using Semi-isotropic pressure coupling with Parrinello-Rahman barostat. I have a few concerns:<br>
<br>
1) On the gromacs website, a webpage mentions that this type of pressure coupling may not be accurate<br>
<br>
</blockquote>
<br></div>
Please provide a link when making this kind of statement.<div class="im"><a href="http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman">http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman</a><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2) It takes a really long time for the system to reach the reference pressure > 500ns. Particularly the Pxx, Pyy terms are very different and take an extremely long time to converge to a common value.<br>
<br>
</blockquote>
<div class="im">integrator = md</div><div class="im">dt = 0.001</div><div class="im">nsteps = 50000000</div><div class="im"><br></div><div class="im">; OUTPUT CONTROL OPTIONS</div>
<div class="im">nstxout = 0 ; No output, except for last frame (coordinates)</div><div class="im">nstvout = 0 ; No output, except for last frame (velocities)</div><div class="im">nstfout = 0 ; No output, except for last frame (forces)</div>
<div class="im">nstlog = 1000000 ; Write every nth step to the log</div><div class="im">nstenergy = 1000000 ; Write energies at every n step</div><div class="im">nstxtcout = 1000000 ; Do not write a compressed tr</div>
<div class="im"><br></div><div class="im">; NEIGHBORSEARCHING PARAMETERS</div><div class="im">nstlist = 10</div><div class="im">ns-type = Grid</div><div class="im">pbc = xyz</div>
<div class="im">rlist = 0.9</div><div class="im"><br></div><div class="im">; OPTIONS FOR ELECTROSTATICS AND VDW</div><div class="im">coulombtype = Cut-off</div><div class="im">rcoulomb = 1.1225</div>
<div class="im">vdw-type = User</div><div class="im">rvdw = 1.1225</div><div class="im">table-extension = 0</div><div class="im"><br></div><div class="im">; Temperature coupling</div>
<div class="im">tcoupl = nose-hoover</div><div class="im">tc-grps = ARAR</div><div class="im">tau_t = 0.1</div><div class="im">ref_t = 120.2717</div>
<div class="im"><br></div><div class="im">; Pressure coupling</div><div class="im">pcoupl = Parrinello-Rahman</div><div class="im">pcoupltype = semiisotropic</div><div class="im">tau-p = 1.0 1.0</div>
<div class="im">compressibility = 1e-5 0 ;Dont know</div><div class="im">ref-p = 69 0</div><div class="im"><br></div><div class="im"><br></div><div class="im">;Generate velocities for startup run</div>
<div class="im">gen_vel =no</div><div class="im">gen_temp =120.2717</div><div class="im">gen_seed =-1</div><div><br></div></div></blockquote><div><div>;Non equilibrium MD steps</div>
<div>freezegrps =ARAR</div><div>freezedim =N N Y </div><div><br></div><div>;Constraints</div><div>constraints = all-bonds</div><div>constraint_algorithm = Lincs</div><div>lincs_order = 4</div>
<div>lincs_iter = 1</div><div>lincs_warnangle = 90 </div><div>;unconstrained_start = no</div><div>;shake_tol = 0.0001</div><div><br></div><div><br></div></div><div><br></div><div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"></div>
What was your equilibration protocol? What are your .mdp settings?<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Pooja<br>
<br>
-- <br>
Quaerendo Invenietis-Seek and you shall discover.<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>