<div dir="ltr"><div class="gmail_quote">Thank you so much for the answer, Prof. van der Spoel.<br><div dir="ltr"><pre>Now I'd like to ask two more questions to you and all gmx-users.<br><br>First, I notice that the number of hydrogen bonds for a given time frame fluctuates slightly, depending on the time range you choose in g_hbond command.<br>
For example, in the same "water" tutorial, if I do the following command:<br>> g_hbond<br>the hbnum.xvg looks like this:<br> 19 363 746<br> 19.1 366 714<br> 19.2 360 696<br>
19.3 371 720<br> 19.4 355 701<br> 19.5 357 686<br> 19.6 357 711<br> 19.7 351 702<br> 19.8 351 712<br>
19.9 360 673<br> 20 363 716<br>However, if I do the following command:<br>> g_hbond -b 18.99 -e 20<br>the hbnum.xvg now looks like this:<br> 19 367 754<br>
19.1 365 715<br> 19.2 358 702<br> 19.3 371 723<br> 19.4 354 714<br> 19.5 369 699<br> 19.6 357 711<br>
19.7 355 700<br> 19.8 351 712<br> 19.9 367 699<br> 20 367 727<br>And if I do:<br>>g_hbond -b 19.99 -e 20<br>the hbnum.xvg now looks like this:<br>
20 358 715<br>You see the number of hydrogen bonds for a given time are different for each command.<br>I wonder why this happens and if there is any significance in it.<br><br>My second question is a bit more complicated.<br>
I'm trying to calculate the average number of hbonds per time frame as a function of z coordinates for two time frames, say t=19.9 and t=20, in the "water" tutorial.<br>So I'm thinking of first creating the index file of hbonds by doing:<br>
> g_hbond -hbn -b 19.9 -e 20<br>, then extracting z coordinates of all the atoms involved in hydrogen bonds at each time frame using g_traj command.<br>Now, at the end of the g_hbond execution, I see the following gromacs comments:<br>
------------------------------------------------------------<br>Reading frame 0 time 19.900<br>Will do grid-seach on 4x4x4 grid, rcut=0.35<br>Last frame 1 time 20.000<br>Found 422 different hydrogen bonds in trajectory<br>
------------------------------------------------------------<br>And the hbond.ndx files indeed lists the 422 "different" hydrogen bonds,<br>However the last two lines of the hbnum.xvg shows:<br> 19.9 358 683<br>
20 365 726<br>which means that there are 358+365 = 723 hbonds over the two time frames. I guess that 422 hbonds in index file count those duplicate hbonds over two time frames only once.<br>Does that mean that I cannot use the hbond.ndx file to properly count total number of hbonds (723) over two time frames?<br>
If so, do I need to obtain hbond.ndx for each single time frame separately to calculate the average number of hbonds per time frame along z axis correctly?<br><br>I hope my questions are clear.<br>Thank you in advance for your kind reply.<br>
<br>Regards,<br>Sung<br><br><br>Sung Hyun Park wrote:<br>><i> Dear Gmx-users,<br></i>><i> <br></i>><i> This may be a dumb question, but I am wondering about the number of <br></i>><i> hydrogen bonds in the "water" tutorial. The system is 216 SPC/E water <br>
</i>><i> molecules in a box, and the number of hydrogen bonds per time frame <br></i>><i> fluctuates around ~350, which gives th number of hydrogen bonds per <br></i>><i> water mlecule to be only ~1.6. Isn't this too low, compared with the <br>
</i>><i> typical number ~3.5 for bulk water mlecule?<br></i>I think it is SPC, and you can multiply the number by 2 since all HB are <br>shared between two mols.<br>><i> <br></i>><i> Thanks,<br></i>><i> Sung<br>
</i>><i> <br></i>><i> <br></i>><i> ------------------------------------------------------------------------<br></i>><i> <br></i>><i> _______________________________________________<br></i>><i> gmx-users mailing list <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">gmx-users at gromacs.org</a><br>
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Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">spoel at xray.bmc.uu.se</a> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">spoel at gromacs.org</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se</a></font></pre>
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