<div>I'm running MD at 300 K.</div>
<div>I want fluid phase.<br><br> </div>
<div><span class="gmail_quote">On 12/13/07, <b class="gmail_sendername">Myunggi Yi</b> <<a href="mailto:myunggi@gmail.com">myunggi@gmail.com</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div>Dear Eric,</div>
<div> </div>
<div>I'm using Berger force field for DOPG (anionic head group).</div>
<div>Is is true for DOPG also?</div>
<div> </div>
<div>The following is my MD input.</div>
<div>I'm getting smaller area per lipid (~52 A^2) than expected (~62).</div>
<div> </div>
<div>What should I change?</div>
<div> </div>
<div>**********************************<br> </div>
<p>; nblist cut-off <br>rlist = 1.6<br>domain-decomposition = no</p>
<p>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>coulombtype = PME<br>rcoulomb-switch = 0<br>rcoulomb = 1.6<br>; Relative dielectric constant for the medium and the reaction field
<br>epsilon_r = 1.0<br>epsilon_rf = 1.0<br>; Method for doing Van der Waals<br>vdw-type = Switch<br>; cut-off lengths<br>rvdw-switch = 1.2<br>rvdw =
1.4<br></p>
<p>******************************************</p>
<div><span class="e" id="q_116d4d4efef1c3c7_1">
<div><br> </div>
<div><span class="gmail_quote">On 12/11/07, <b class="gmail_sendername">Eric Jakobsson</b> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:jake@ncsa.uiuc.edu" target="_blank">jake@ncsa.uiuc.edu
</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Several points:<br><br>What is called the Berger force field was<br>actually developed by See-Wing Chiu in our lab
<br>and presented in a 1995 paper. The Berger et al<br>paper tested this force field against another<br>candidate and found that it was better, and that<br>is the paper that has been cited ever since.<br><br>See-Wing did tests of the necessary VDW cut-off
<br>for accuracy against what seemed like the most<br>sensitive test, the value of the dipole potential<br>at the water-lipid interface, and concluded that<br>one should use a cut-off of at least 18 angstroms.<br><br>The van der Waals parameters for the hydrocarbon
<br>tails were reparameterized in a paper we<br>published a few years ago, and in that paper we<br>verified that the 18 angstrom cutoff was required<br>for an accurate liquid hydrocarbon simulation also.<br><br>Recently See-Wing has reparameterized the van der
<br>Waals parameters in the lipid head groups, using<br>specific volumes of liquids comprised of small<br>molecules that are part of the head group. The<br>resulting force fields, which retain the partial<br>charges of the Berger-Chiu field, work very well
<br>in replicating x-ray structure factors of lipids<br>with various chain compositions, but he has not<br>yet tried to do gel phase--that would be<br>interesting. The journal ms. is still sitting on<br>my desk, I am afraid, but there is a pretty good
<br>description of the parameterization in a chapter<br>in a book that Scott Feller is editing, which we<br>can send on request, as well as the lipid<br>complete force field in itself. We believe it is<br>state of the art at this time.
<br><br>Best,<br>Eric<br>At 10:22 AM 12/11/2007, you wrote:<br>>Hi Steffen,<br>><br>>thanks a lot for your reply.<br>>>-what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm<br>>>twin range cutoff for working properly. Are you using PME for
<br>>>electrostatics?<br>>><br>>I used a LJ-cutoff at 1.0nm. That's what was<br>>used for the original Berger-Paper (*O Berger, O<br>>Edholm and F Jähnig, */Biophysical Journal/ 72:<br>>2002-2013 (1997). Shouldn't this be all right?
<br>><br>>And I used PME (which was indeed not used in the original work.<br>><br>>>-how did you set up the pressure coupling?<br>>><br>>I used weak coupling (tau=1.0ps)<br>><br>>>-900 waters are not really much, the head groups will probably interact
<br>>>with their mirror images due to pbc. Try a lot more (thought about<br>>>10000?) for having a "real" bilayer in a solution.<br>>><br>>I also tried with more water, the gel phase did not appear either.
<br>><br>>> >From my experience, the Berger lipids are well defined for a specific<br>>>temperature, but if you go up/down the temperature scale, they are not<br>>>really following the experimental values/phase behaviour. By the way:
<br>>>experimental data on lipid order parameters varies considerably<br>>>throughout the complete literature, so don't rely onto that too much as<br>>>well.<br>>>Sorry for giving more questions than answers, but that's the shitty part
<br>>>with lipid bilayers in MD...<br>>>Steffen<br>>><br>>Thanks again,<br>>Jochen<br>><br>><br>><br>>--<br>>************************************************<br>>Jochen Hub<br>>Max Planck Institute for Biophysical Chemistry
<br>>Computational biomolecular dynamics group<br>>Am Fassberg 11<br>>D-37077 Goettingen, Germany<br>>Email: jhub[at]gwdg.de<br>>************************************************<br>>_______________________________________________
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</a><br><br>---------------------------------<br>Eric Jakobsson, Ph.D.<br>Professor, Department of Molecular and<br>Integrative Physiology, and of Biochemistry, and<br>of the Center for Biophysics and Computational Biology
<br>Senior Research Scientist, National Center for Supercomputing Applications <br>Professor, Beckman Institute for Advanced Science and Technology<br>3261 Beckman Institute, mc251<br>University of Illinois, Urbana, IL 61801
<br>ph. 217-244-2896 Fax 217 244 9757<br><br><br><br><br>_______________________________________________ <br>gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">
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http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br></span></div>-- <br>Best wishes, <br><br>MYUNGGI YI<br>==================================<br>KLB 419<br>Institute of Molecular Biophysics
<br>Florida State University<br>Tallahassee, FL 32306<br><br>Office: (850) 645-1334<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.scs.fsu.edu/~myunggi" target="_blank">http://www.scs.fsu.edu/~myunggi
</a></blockquote></div><br><br clear="all"><br>-- <br>Best wishes,<br><br>MYUNGGI YI<br>==================================<br>KLB 419<br>Institute of Molecular Biophysics<br>Florida State University<br>Tallahassee, FL 32306
<br><br>Office: (850) 645-1334<br><a href="http://www.scs.fsu.edu/~myunggi">http://www.scs.fsu.edu/~myunggi</a>