Dear all, <br><br>I have reported a week ago update about my troubles with octanol/water slab and pulling simulations, where COM code starts to report a wrong distances between centre-of-masses between two groups when bigger box (see bellow) is used. <br>
<br>So far, smaller box cured our actual calculation problems, but I am still curious why g_dist and pullx.xvg are giving so different values, when I enlarge the simulation box? <br><br>Best wishes<br>Karel Berka<br><br>Original mail down there <br>
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Dear all,<br>
<br>
We have tested more strange behavior of constraints from pull code for<br>
calculation of free energy differences small molecule on DOPC membrane and<br>
octanol slab.<br>
As I have reported previously, while the errors in free energy differences<br>
on DOPC were rather small, the errors on octanol were strangely high.<br>
<br>
We have prepared smaller slabs (as Chris Neale suggested) of octanol with<br>
comparable size of box and we have also tried to analyze the position of<br>
centres either via pullx.xvg provided by pull code, but also by g_dist<br>
utility and to our surprise, size matters. A lot.<br>
(Same groups were used in mdp for pull and for g_dist analysis, only<br>
distances in z-axis is shown)<br>
<br>
DOPC, 128 molecules, box size 6.2 6.4 8.3 , position of small molecule on<br>
the edge of membrane<br>
Time(ps) pullf.xvg dist.xvg<br>
0.00 -0.12416 -0.12436<br>
1.00 -0.12416 -0.12433<br>
2.00 -0.12416 -0.12428<br>
3.00 -0.12416 -0.12430<br>
4.00 -0.12416 -0.12430<br>
5.00 -0.12416 -0.12432<br>
6.00 -0.12416 -0.12434<br>
7.00 -0.12416 -0.12449<br>
As can be seen, the variation of distances reported by these two programs is<br>
not perfect, but it is rather ok with precision of about 0.001 nm.<br>
<br>
Octanol, 957 molecules, box size 5.7 5.9 13.7, position is similar on the<br>
edge of slab, errors in free energy profiles are mainly here.<br>
Time(ps) pullf.xvg dist.xvg<br>
0.00 -2.81855 -3.41133<br>
1.00 -2.81076 -3.44213<br>
2.00 -2.82005 -3.27949<br>
3.00 -2.81856 -3.35097<br>
4.00 -2.82016 -3.50378<br>
5.00 -2.81849 -3.63261<br>
6.00 -2.81855 -3.60058<br>
7.00 -2.81870 -3.80251<br>
8.00 -2.81859 -3.32790<br>
9.00 -2.81849 -3.24329<br>
10.00 -2.81855 -3.28394<br>
21.00 -2.81855 -4.02524<br>
Here, the distances reported by pull code and by g_dist are completely<br>
different with differences in about 1 nm! Visual inspection in VMD says that<br>
small molecule is highly mobile a actual distances are reported rightly by<br>
g_dist program.<br>
Strangely enough, when we put distance measured by g_dist as a start into<br>
the pull code without guessing the distances, but this also did not worked,<br>
since the molecule tried to be at some completely different position and the<br>
simulation crashed as the molecule speeded up.<br>
<br>
Octanol, 475 molecules, box size 5.5 5.5 9.5, position also on the edge of<br>
the slab<br>
Time(ps) pullf.xvg dist.xvg<br>
0.00 -0.49996 -0.49989<br>
1.00 -0.49996 -0.49988<br>
2.00 -0.49996 -0.49981<br>
3.00 -0.49996 -0.49981<br>
4.00 -0.49996 -0.50001<br>
5.00 -0.49996 -0.49987<br>
6.00 -0.49996 -0.49986<br>
7.00 -0.49996 -0.49994<br>
8.00 -0.49997 -0.49988<br>
9.00 -0.49996 -0.49980<br>
10.00 -0.49996 -0.49988<br>
Smaller box cured miraculously the problem, since here the difference is<br>
similarly small as in DOPC case.<br>
<br>
However just to remind another ache we had with octanol slab, in case of<br>
octanol, the size of box in xy plane had to be held constant as the box<br>
narrowed thorough the whole simulation when in anisotropic NPT ensemble.<br>
<br>
Why g_dist and pullx show so different results in large box, I still do not<br>
understand. Any suggestions?<br>
And possibly any suggestions whether our box narrowing in case of octanol is<br>
common or do we have another devil hidden there?<br>
<br>
Best wishes<br>
--<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 clear="all"></div>