Hi,<div><br></div><div>As mentioned in the reference below, changing rlist to 1.4 (greater than the nonbonded cutoffs) and changing nstlist to 5 appears to solve the problem.<br><div><br></div><div><ol>
<li>Siewert J. Marrink et al., “Comment on “On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models” by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934,” <span style="font-style:italic;">Physical Chemistry Chemical Physics</span> 12, no. 9 (2010): 2254. <span class="Z3988" title="url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rft_id=info%3Adoi/10.1039/b915293h&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Comment%20on%20%E2%80%9COn%20using%20a%20too%20large%20integration%20time%20step%20in%20molecular%20dynamics%20simulations%20of%20coarse-grained%20molecular%20models%E2%80%9D%20by%20M.%20Winger%2C%20D.%20Trzesniak%2C%20R.%20Baron%20and%20W.%20F.%20van%20Gunsteren%2C%20Phys.%20Chem.%20Chem.%20Phys.%2C%202009%2C%2011%2C%201934&rft.jtitle=Physical%20Chemistry%20Chemical%20Physics&rft.stitle=Phys.%20Chem.%20Chem.%20Phys.&rft.volume=12&rft.issue=9&rft.aufirst=Siewert%20J.&rft.aulast=Marrink&rft.au=Siewert%20J.%20Marrink&rft.au=Xavier%20Periole&rft.au=D.%20Peter%20Tieleman&rft.au=Alex%20H.%20de%20Vries&rft.date=2010&rft.pages=2254&rft.issn=1463-9076"> </span></li>
</ol><br><div class="gmail_quote">On Tue, Jun 15, 2010 at 10:44 PM, Michael Lerner <span dir="ltr"><<a href="mailto:mglerner@gmail.com">mglerner@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse;color:rgb(51, 51, 51)">Hi,<div><br></div><div>I want to run some MARTINI DPPC/water simulations using the microcanonical (NVE) ensemble.</div>
<div><br></div><div>I ran a long NVT simulation to make sure things were fully equilibrated. Then I took the .gro file as input and removed the temperature/pressure coupling options from my .mdp file. I also removed the center-of-mass-removal options. Unfortunately, the temperature decreases rather quickly from 323K to below 200K. I've included my .mdp file below. Is there something obviously wrong with it? If not, are there other things I should try?</div>
<div><br></div><div>Thanks,</div><div><br></div><div>-Michael</div><div><br></div><div>P.S. I recently changed the email address that I use to subscribe to gmx-users. My apologies if this gets sent to the list twice as part of that.</div>
<div><br></div><div><div>Pcoupl = no </div><div>DispCorr = No </div><div>gen_vel = no </div><div>integrator = md </div><div>nstvout = 100000 </div><div>epsilon_surface = 0 </div><div>nstlog = 2500 </div><div>nstenergy = 2500 </div>
<div>comm_mode = None </div><div>xtc_precision = 100 </div><div>rvdw_switch = 0.9 </div><div>epsilon_r = 15 </div><div>nstxtcout = 2500 </div><div>ewald_rtol = 1e-05 </div><div>continuation = yes </div><div>constraints = none </div>
<div>nsteps = 500000 </div><div>vdw_type = Shift </div><div>tcoupl = no </div><div>rlist = 1.2 </div><div>lincs_warnangle = 30 </div><div>xtc-grps = Prot </div><div>lincs_order = 4 </div><div>dt = 0.02 </div><div>tinit = 0.0 </div>
<div>coulombtype = Shift </div><div>shake_tol = 0.0001 </div><div>nstlist = 5 </div><div>rcoulomb_switch = 0.0 </div><div>morse = no </div><div>nstxout = 100000 </div><div>annealing = no </div><div>constraint_algorithm = Lincs </div>
<div>pbc = xyz </div><div>rcoulomb = 1.2 </div><div>compressibility = 5e-5 5e-5 </div><div>energygrps = Prot SOL </div><div>ns_type = grid </div><div>nstfout = 0 </div><div>rvdw = 1.2 </div></div></span><br><font color="#888888">-- <br>
Michael Lerner, Ph.D.<br>
IRTA Postdoctoral Fellow<br>Laboratory of Computational Biology NIH/NHLBI<br>5635 Fishers Lane, Room T909, MSC 9314<br>Rockville, MD 20852 (UPS/FedEx/Reality)<br>Bethesda MD 20892-9314 (USPS)<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Michael Lerner, Ph.D.<br>IRTA Postdoctoral Fellow<br>Laboratory of Computational Biology NIH/NHLBI<br>5635 Fishers Lane, Room T909, MSC 9314<br>Rockville, MD 20852 (UPS/FedEx/Reality)<br>
Bethesda MD 20892-9314 (USPS)<br>
</div></div>