Hi Tsjerk,<br><br>My gromacs is 4.0.4.<br><br>As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess the box is not defined yet. The pdb was taken from the trajectory of AMBER simulation, so it starts with the keyword "REMARK". How do I include box dimensions in pdb file then? Just add "CRYST1 24 24 24" in the first line? By the way is it CRYST1 or CRYSTL?<br>
<br>And the command I was running was "g_mindist -f 1001.pdb -n 1001.ndx -od 1001_C".<br><br>Dian<br><br><div class="gmail_quote">On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Dian,<br>
<br>
Which version of gromacs are you using? Can you assert that the pdb<br>
file has the correct box? It should have a line starting with CRYST1<br>
(grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2 I think)<br>
didn't write the CRYST1 record, and thus disallow PBC related<br>
operations.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Thu, Mar 4, 2010 at 8:08 AM, Dian Jiao <<a href="mailto:oscarjiao@gmail.com">oscarjiao@gmail.com</a>> wrote:<br>
> The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about<br>
> 31 A away from the closest water in the box. But if it is periodic,<br>
> shouldn't there be waters near the dummy too?<br>
><br>
> On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
> wrote:<br>
>><br>
>> On 4/03/2010 11:30 AM, Dian Jiao wrote:<br>
>>><br>
>>> Hi Gromacs users,<br>
>>><br>
>>> I was trying to compute minimum distance between groups in a cubic water<br>
>>> box with g_mindist using periodic boundary condition. In order to test<br>
>>> this, I added one more "atom" which is far away from any of the other<br>
>>> atoms in the pdb file. The mindist between that atom and all the waters<br>
>>> were computed. The output of g_mindist is 3.089281e+00. (the unit is nm,<br>
>>> right?)<br>
>><br>
>> You haven't said how big your box is, or how far "far away" is, so we<br>
>> can't tell whether you think 3nm is too big, too small, etc.<br>
>><br>
>>> The manual shows that pbc is one of the option of g_mindist, but isn't<br>
>>> the default "yes"? I even tried with "-pbc" in the command, still did<br>
>>> not work. Can anyone tell me how to turn on PBC in g_mindist?<br>
>><br>
>> See g_mindist -h. The -pbc flag turns PBC on, -nopbc turns it off.<br>
>><br>
>> Mark<br>
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</div></div>> --<br>
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<br>
<br>
</div><font color="#888888">--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
Computational Chemist<br>
Medicinal Chemist<br>
Neuropharmacologist<br>
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