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<div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Dear Justin </span></font><br>Thank you for your responses, but it still is not clear to me why is that happening<br>
<br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> I don't see any real problem here. The DOPC membrane probably holds its shape</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> better than the octanol slab and thus the reference position (which determines</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> the constraint) is less mobile. </span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">That is certain. When we were running free simulation, the box started to narrow. Therefore we have frozen the box in xy plane. </span></font></div>
<div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> As such, the constraint is more stable in DOPC</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> than in octanol. The slight bump in the octanol system amounts to a change of</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> 0.16%, which I'd say is quite small. </span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">The trouble is, that during next 10 ns the distance was between 2.0 - 4.0 and molecule moved outside of the ocatnol slab and inside, which is then useless for calculation of PMF. </span></font></div>
<div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> You're also looking at the first few</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">>frames of the simulation, which may amount to equilibration, but you haven't</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> mentioned if you've done anything prior to this run.</span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Previously, a free simulation with molecule on slab was run for 20 ns, from which frame with small molecule at specidied depth was taken, so I suppose, that the start is equilibrated. <br>
</span></font><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> As long as there is no systematic change in position, I'd say there's no problem.</span></font><br>
<br></div><div id=":z1">Unfortunately, there is as I have said before. </div><div id=":z1"><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">-Justin</span></font><br>
<br></div><div id=":z1">Dear Chris, </div><div id=":z1">thank you for responses as well. <br><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> I agree that Justin is probably correct, although constraints should</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> technically work just fine with a highly dynamic reference group. Any</span></font><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> problems should show up as the system blowing up, but not in correctly</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> setting the position. </span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">I hope, that the position is set up ok, as it stays steady in DOPC. </span></font></div>
<div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> I think that the problems can arise, however,</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> when you have multiple competing constraints. You might, for example,</span></font><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> try without constraining the octane bonds -- I think that you should</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> get perfect match in that case. </span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">I will try. </span></font></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><meta http-equiv="content-type" content="text/html; charset=utf-8"><span class="Apple-style-span" style="font-family: arial; border-collapse: separate; ">The erroneous movement of molecule seems to be enhanced within XY-plane frozen. </span></span></font></div>
<div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">The curious thing is however, that when I did not constrain size of xy-plane, then the distance to the COM of slab is not changing much (only last digit changes), which in comparison to frozen XY-plane, where there is huge movement above the slab and within is rather ok to me. Unfortunately, I have the issue with narrowing of the box in the unconstrained XYplane simulation, which also destroys any attempts for PMF as I have mentioned before. </span></font></div>
<div id=":z1"><br></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> Also, it is worth comparing in single</span></font><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> and double precision.</span></font><br>
<br></div><div id=":z1">I will try this either.</div><div id=":z1"><br></div><div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> Still, I am not sure that you actually did a proper comparison for the</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> following 2 reasons:</span></font><br>><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; ">1. you have apparently different masses for the pulled group:</span><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> Pull group 1: 15 atoms, mass 194.194</span></font><br><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> Pull group 1: 15 atoms, mass 146.146</span></font><br>
<br></div><div id=":z1">The difference is not much in my opinion, while molecules tested are similar in size and are run in DOPC ok both of them. </div><div id=":z1"><br></div><div id=":z1">> <span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; ">2. you used very different starting depth offsets: -2.81855 is not</span></div>
<div id=":z1"><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> very close to -1.60929</span></font><br><br></div><div id=":z1">The difference is in the size of OCT slab (thick) and DOPC (narrow) and the trouble is in the vicinity of the water phase, so the distances are (and should be) different. </div>
<div id=":z1"><br><span class="Apple-style-span" style="font-family: arial, sans-serif; border-collapse: collapse; ">> PS: I would personally prefer if you avoided jumping directly to a bug</span> <font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">report unless you are sure of it. There is always at least the</span></font><br>
<font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">> possibility that you are not using the code correctly.</span></font><br><br></div><div id=":z1">
Certainly and I appreciate two directions you gave me to try - at least I will look inside octanol topology since I did not used octanol before our tries of logP. However, I did not say anything about bug (I even searched for term in my mail and I did not find it)</div>
<div id=":z1"><br></div><div id=":z1">But how to set the box properly then? </div><div id=":z1"><br></div><div id=":z1"><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; ">> Chris.</span></div>
<div id=":z1"><br></div><div id=":z1">Thank you both</div><div id=":z1">Karel </div><div id=":z1"><br></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>
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