Hi all, <div>I am simulating drugs in water/lipid bilayer environment. </div><div>And I have noticed that when I put drug into the middle of the box, it is moving rather quickly around until it finds a x or y boundary. Then it stays there moving not much on both sides of the box. <br clear="all">
In the first time it looked fine to me as I was supposing to be normal. </div><div>But then I realized, that it stays there much longer, then it was moving before in the middle of the box. </div><div><br></div><div>I have looked into the other simulations and i found, that it makes the same behaviour - if it goes to the box boundary, then it stays there. I was thinking that it means, that the membrane is not ok in this region, but nay by eye, the periodic image of membrane in VMD is ok and the boundary is indistiguishable. </div>
<div><br></div><div>Do you have any idea what might be wrong? If it is wrong? </div><div><br></div><div>I use DOPC membrane in G56a6 from 1. Siu, S. et al. Biomolecular simulations of membranes: Physical properties from different force fields. JCP <b>128</b>, (2008). </div>
<div>and my mdp is here.</div><div><div>coulombtype = PME ; see 8.4.1</div><div>rcoulomb = 1.0 ; see 8.4.1</div><div>rvdw = 1.1 ; see 8.4.1</div><div>fourierspacing = 0.15 ; see 8.4.1</div><div>ewald_rtol = 1e-5 ; see 8.4.1</div>
<div>pme_order = 4 ; interpolation order for PME</div><div>optimize_fft = yes ; see 8.4.1</div><div><br></div><div>;</div><div>; Couplings</div><div>; Berendsen temperature coupling given by equation (1.12) of five</div><div>
molecular groups to ref_t with relaxation time tau_t.</div><div>Tcoupl = V-rescale ;</div><div>tc-grps = System</div><div>tau_t = 0.1 </div><div>ref_t = 300 </div><div>; Energy monitoring of groups:</div>
<div>energygrps = DRG DOPC SOL </div><div>;</div><div>; Berendsen pressure coupling given by equation (1.13) is on</div><div>pcoupl = berendsen</div><div>pcoupltype = anisotropic ; box remains rectangular</div><div>tau_p = 10 ; pressure coupling time parameter</div>
<div>compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ; compresibility </div><div>ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 ;reference pressure </div><div>; </div></div><div>-- <br>Zdraví skoro zdravý<br>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><br>****************************************************************<br>
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