<div>Thanks, Tsjerk.</div><div>Exactly as what you said, it was because split of molecules over</div><div>the boundary. It runs smoothly right now as I started with a dodecahedron box.</div><div> </div><div>best,</div><div>
Zhenlong<br><br></div><div class="gmail_quote">On Thu, Oct 6, 2011 at 12:24 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left-color: rgb(204, 204, 204); border-left-width: 1px; border-left-style: solid;" class="gmail_quote">
Hi Zhenlong,<br>
<br>
I guess that some molecules got split over the boundaries during<br>
equilibration. You have to make them whole before changing the box.<br>
Better to start off with a rhombic dodecahedron though.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Thu, Oct 6, 2011 at 6:29 PM, zhenlong li <<a href="mailto:zxl1000@gmail.com">zxl1000@gmail.com</a>> wrote:<br>
> Dear all,<br>
> My system is based on Martini, needs a dodehedron box.<br>
> Initially, it was minimized and equilibrated with a cubic box smoothly. Then<br>
> I used the follow command to<br>
> translate the box in to dodehedron:<br>
> editconf -f f0.gro -bt dodecahedron -d 2 -o vesdode.gro<br>
> But with this change, the simulation always blows up with the message below.<br>
><br>
> Since those atoms are most at the boundary of the box, I think it is because<br>
> the overlap of boundary atoms<br>
> with the new box type. I tried different value for -d and -box, but still<br>
> have the same problem.<br>
><br>
> Can anybody give me any hint to fix this?<br>
><br>
> Thanks a lot!<br>
> Zhenlong<br>
><br>
> ---------------------------------------------------------------------------------------------------------------------------------<br>
> Making 3D domain decomposition 7 x 4 x 3<br>
><br>
> A list of missing interactions:<br>
> Bond of 79872 missing 7<br>
> G96Angle of 50688 missing 9<br>
><br>
> Molecule type 'DPPC'<br>
> the first 10 missing interactions, except for exclusions:<br>
> G96Angle atoms 6 7 8 global 37638 37639 37640<br>
> Bond atoms 7 8 global 37639 37640<br>
> G96Angle atoms 10 11 12 global 37642 37643 37644<br>
> Bond atoms 11 12 global 37643 37644<br>
><br>
> Molecule type 'DUPC'<br>
> the first 10 missing interactions, except for exclusions:<br>
> G96Angle atoms 10 11 12 global 38446 38447 38448<br>
> Bond atoms 11 12 global 38447 38448<br>
><br>
> Molecule type 'DPPC'<br>
> the first 10 missing interactions, except for exclusions:<br>
> G96Angle atoms 3 5 6 global 43395 43397 43398<br>
> Bond atoms 5 6 global 43397 43398<br>
> G96Angle atoms 5 6 7 global 43397 43398 43399<br>
><br>
> Molecule type 'DUPC'<br>
> the first 10 missing interactions, except for exclusions:<br>
> G96Angle atoms 6 7 8 global 45330 45331 45332<br>
> Bond atoms 7 8 global 45331 45332<br>
><br>
> Molecule type 'DUPC'<br>
> the first 10 missing interactions, except for exclusions:<br>
> G96Angle atoms 5 6 7 global 57173 57174 57175<br>
> Bond atoms 6 7 global 57174 57175<br>
> G96Angle atoms 6 7 8 global 57174 57175 57176<br>
><br>
> Molecule type 'DPPC'<br>
> the first 10 missing interactions, except for exclusions:<br>
> G96Angle atoms 6 7 8 global 63822 63823 63824<br>
> Bond atoms 7 8 global 63823 63824<br>
><br>
><br>
</div></div>> --<br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
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