<div>Hello Chris, thanks for your attention.</div><div>I'm sending you some links to some tests </div><div>I performed. As I said you will notice that </div><div>depending on the parameter used my simulation </div><div>
shows PMF profiles quite different. Especially what </div><div>concerns to the difference between the use or not of the PBC.</div><div><br></div><div><a href="https://sites.google.com/site/fileti/files/test1.jpg" target="_blank">https://sites.google.com/site/fileti/files/test1.jpg</a></div>
<div><a href="https://sites.google.com/site/fileti/files/test2.jpg" target="_blank">https://sites.google.com/site/fileti/files/test2.jpg</a></div><div><a href="https://sites.google.com/site/fileti/files/histo.png" target="_blank">https://sites.google.com/site/fileti/files/histo.png</a></div>
<div><br></div><div>I have constructed two very similar topologies (ben-a.itp and ben-b.itp) </div><div>where I put a virtual site in the center of benzene. </div><div>This sites were restrained to keep my molecules </div>
<div>fixed distance desired.</div><div><br></div><div>The basic details of the simulations are given below:1000</div><div><br></div><div><div>define = -DPOSRES</div><div>integrator = sd</div>
<div>tinit = 0</div><div>dt = 0.002</div><div>nsteps = 5000000 or 500000</div><div>comm-mode = angular</div><div>nstcomm = 1</div>
<div>comm-grps = System</div><div>bd-fric = 1</div><div>ld-seed = 1993</div><div>nstlist = 5</div><div>ns_type = simple</div><div>pbc = no or xyz</div>
<div>periodic_molecules = no</div><div>rlist = 0</div><div>coulombtype = Cut-off</div><div>vdw-type = Cut-off</div><div>rvdw = 0</div><div>DispCorr = no</div>
<div>Tcoupl = Nose-Hoover</div><div>tc_grps = system</div><div>tau_t = 0.1</div><div>ref_t = 300</div><div>Pcoupl = no</div><div>
pcoupltype = isotropic</div>
<div>tau_p = 1.0</div><div>compressibility = 4.5e-5</div><div>ref_p = 1.0</div><div>constraints = all-bonds</div><div>constraint_algorithm = lincs</div><div>
<br></div><div>; COM PULLING </div><div>pull = umbrella</div><div>pull_geometry = distance</div><div>pull_dim = N N Y</div><div>pull_r1 = 1</div><div>
pull_r0 = 1.5</div><div>pull_constr_tol = 1e-06</div><div>pull_start = yes</div><div>pull_nstxout = 10</div><div>pull_nstfout = 10</div><div>pull_ngroups = 1</div>
<div>pull_group0 = BENa</div><div>pull_weights0 = </div><div>pull_pbcatom0 = 0</div><div>pull_group1 = BENb</div><div>pull_weights1 = </div><div>pull_pbcatom1 = 0</div>
<div>pull_vec1 = 0 0 1</div><div>pull_init1 = 0</div><div>pull_rate1 = 0.0</div><div>pull_k1 = 1700 or </div></div><div><br></div>_______________________________________<br>
Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC — CCNH<br>Av. dos Estados, 5001<br>Santo André - SP - Brasil<br>CEP 09210-971<br>+55.11.4996-0196<br><a href="http://fileti.ufabc.edu.br" target="_blank">http://fileti.ufabc.edu.br</a><br>
<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Dear Eudes:<br>
<br>
Can you please elaborate on your description? What .mdp options are<br>
you using? What exactly do your curves look like (you can post<br>
pictures to photobucket or some other online service and link them<br>
here)? If you suspect that you are doing something wrong, then we need<br>
to understand exactly what you are doing and exactly what you are<br>
seeing in order to help.<br>
<br>
Chris.<br>
<br>
-- original message --<br>
<br>
Hi gmx-users,<br>
I'm trying to simulate a umbrella sampling PMF between two benzene<br>
molecules<br>
in vacuum. My protocol is working fine, my histograms have good overlap and<br>
the curves I have got are quite reasonable.<br>
<br>
However I have noticed that some options in my .mdp file can significantly<br>
change<br>
the depth of the well. Also the curves can not go to zero at long distances.<br>
For example, if I use PBC I get a reasonably good value for the minimum of<br>
the PMF<br>
but from a certain separation it starts to increase slightly in a linear<br>
fashion<br>
instead of going to zero. On the other hand, if I make pbc = no, I get an<br>
acceptable curve,<br>
with the PMF going to zero, but with the minimum too high.<br>
<br>
Someone could give me any tips on the best set of parameters to calculate<br>
this PMF in a vacuum?<br>
bests<br>
eef<br>
<br>
<br></blockquote></div>