Dear all, <div><br></div><div>we are trying to simulate molecule in specified depth in octanol to calculate logP. </div><div>for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp: </div>
<div><br></div><div><div>integrator = md</div><div>dt = 0.002</div><div>tinit = 0</div><div>nsteps = 5125000 ; 10.250 ns</div><div>nstcomm = 1</div><div>comm_mode = Linear</div>
<div>; Output parameters</div><div>nstxout = 0 ; every 1 ns</div><div>nstvout = 0</div><div>nstfout = 0</div><div>nstxtcout = 500 ; every 1 ps</div><div>nstenergy = 500</div>
<div>; Bond parameters</div><div>constraints = all-bonds</div><div>; Single-range cutoff scheme</div><div>nstlist = 5</div><div>ns_type = grid</div><div>rlist = 1.4</div><div>rcoulomb = 1.4</div>
<div>rvdw = 1.4</div><div>; PME electrostatics parameters</div><div>coulombtype = PME</div><div>fourierspacing = 0.12</div><div>fourier_nx = 0</div><div>fourier_ny = 0</div><div>fourier_nz = 0</div>
<div>pme_order = 4</div><div>ewald_rtol = 1e-5</div><div>optimize_fft = yes</div><div>; Berendsen temperature coupling is on in two groups</div><div>Tcoupl = V-rescale</div><div>tc_grps = System</div>
<div>tau_t = 0.1</div><div>ref_t = 310</div><div>; Pressure coupling is on</div><div>Pcoupl = berendsen</div><div>pcoupltype = anisotropic ; anisotropic pressure coupling</div><div>tau_p = 10</div>
<div>compressibility = 0 0 4.5e-5 0 0 0 ; since octanol tries to separate from water and shortening xy plane</div><div>ref_p = 1.0 1.0 1.0 0 0 0 </div><div>; Pull code</div><div>pull = constraint ;</div>
<div>pull_geometry = distance ; Pull along the vector connecting the two groups. Components can be selected with pull_dim.</div><div>pull_dim = N N Y ; put potential only to axis z</div></div><div><div>
pull_start = yes ; define initial COM distance > 0</div><div>pull_ngroups = 1 ; one group to pull</div><div>pull_group0 = OCT ; reference group (can be empty to set it to 0,0,0)</div>
<div>pull_group1 = DRG</div><div>pull_rate1 = 0 ; 0.01 nm per ps = 10 nm per ns = 10 m per s</div><div>pull_k1 = 2000 ; kJ mol^-1 nm^-2</div></div><div><br></div><div>however when I list pull-x.xvg I obtain:</div>
<div><div>@ s0 legend "0 Z"</div><div>@ s1 legend "1 dZ"</div><div>0.0000 6.06871 -2.81855</div><div>0.0200 6.07793 -2.81861</div><div>0.0400 6.08787 -2.81856</div><div>0.0600 6.08462 -2.81855</div>
<div>0.0800 6.10028 -2.82007</div><div><br></div></div><div>The situation is even more strange when almost the same mdp with DOPC membrane works fine as can be seen in pull-x.xvg:</div><div><div>0.0000 3.72735 -1.60929</div>
<div>0.0200 3.72727 -1.60929</div><div>0.0400 3.7272 -1.60929</div><div>0.0600 3.72716 -1.60929</div><div>0.0800 3.72715 -1.60929</div><div>0.1000 3.72717 -1.60929</div></div><div><br></div><div>Differences in the working case in mdp are only this:</div>
<div><div>compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 </div><div>ref_p = 1.0 1.0 1.0 0 0 0 </div></div><div>pull_group0 = DOPC</div>
<div><br></div><div>Strangerly enough - the same happens in GMX4.0.7 and in GMX4.5.3</div><div><br></div><div>I wonder where the difference is, as both logs states that </div><div><div>Will apply constraint COM pulling in geometry 'distance'</div>
<div>between a reference group and 1 group</div><div>Pull group 0: 6912 atoms, mass 100624.859</div><div>Pull group 1: 15 atoms, mass 194.194</div></div><div><br></div><div><div>Will apply constraint COM pulling in geometry 'distance'</div>
<div>between a reference group and 1 group</div><div>Pull group 0: 9570 atoms, mass 124631.453</div><div>Pull group 1: 15 atoms, mass 146.146</div></div><div><br></div><div>Where should I look and repair? </div><div>
<br></div><div>Thank you in advance</div><div>Karel</div><div><br></div><div><br></div><div>Zdraví skoro zdravý</div><div>Karel "Krápník" Berka<br><br>****************************************************************<br>
RNDr. Karel Berka, Ph.D.<br>Palacký University in Olomouc<br>Faculty of Science<br>Department of Physical Chemistry<br>tř. 17. listopadu 1192/12<br>771 46 Olomouc<br>tel: +420-585634769 <br>fax: +420-585634769<br>e-mail: <a href="mailto:karel.berka@upol.cz">karel.berka@upol.cz</a><br>
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