<div dir="ltr">Yes, mdrun applies PBC at every step and some atoms at top/bottom will translate to the bottom/top at some steps. So in dynamics simulation, the polarization given by gromacs is meaningless. Is there anyway I can apply PBC without translation ( e.g. change the box center automatically to avoid translation) ? <br clear="all">
Thanks,<br>Shuangxing Dai<br>
<br><br><div class="gmail_quote">On Wed, Jul 28, 2010 at 11:46 AM, Vitaly Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Shuangxing,<br>
<br>
For my case, I wrote a script just to do +/- LBOX when x>LBOX || x <<br>
0. I am not well familiar with polarization algorithm in gromacs but<br>
it seems not to be a problem during a run since mdrun applies PBC at<br>
every step. Maybe I am false here...<br>
<font color="#888888"><br>
Vitaly<br>
</font><div><div></div><div class="h5"><br>
<br>
On Wed, Jul 28, 2010 at 6:35 PM, Shuangxing Dai <<a href="mailto:shuangxingdai@gmail.com">shuangxingdai@gmail.com</a>> wrote:<br>
> I think I met the same problem. When apply periodicity to the system, some<br>
> atoms will translate to the other side of the box, and this gives wrong<br>
> polarization values (especially in dynamic simulations). Anyone has idea how<br>
> to prevent this and get correct polarization in dynamics?<br>
> Thanks,<br>
> Shuangxing Dai<br>
><br>
><br>
> On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>> wrote:<br>
>><br>
>> Hi,<br>
>><br>
>> Is there an option in any gromacs utility to apply periodicity to the<br>
>> output configuration or trajectory? I want to get all the coordinates<br>
>> just within an elementary box, between 0 and LBOX in spite of any<br>
>> details of the system.<br>
>><br>
>> For example, "editconf -no(pbc)" does not do its work since after<br>
>> processing negative coordinates are sometimes present as well as those<br>
>> bigger than LBOX.<br>
>><br>
>> Vitaly<br>
>><br>
>> Dr. Vitaly Chaban<br>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the<br>
>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
><br>
</div></div></blockquote></div><br></div>