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3.2.1 does not work for pbc=full with constraints. Check here for
getting CVS version<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/developer/cvs_usage.php">http://www.gromacs.org/developer/cvs_usage.php</a><br>
<br>
<div class="moz-signature"><i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
</div>
<br>
<br>
Malin Bergenstrahle wrote:
<blockquote cite="mid4325B45C.3020404@kth.se" type="cite"><br>
<br>
<br>
------------------------------
<br>
<br>
Message: 7
<br>
Date: Mon, 12 Sep 2005 23:38:01 +0800
<br>
From: Yang Ye <a class="moz-txt-link-rfc2396E" href="mailto:leafyoung81-group@yahoo.com"><leafyoung81-group@yahoo.com></a>
<br>
Subject: Re: [gmx-users] constraints and pbc=full
<br>
To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
<br>
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:4325A0D9.6030008@yahoo.com"><4325A0D9.6030008@yahoo.com></a>
<br>
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<br>
<br>
Malin Bergenstrahle wrote:
<br>
<br>
<br>
>> Hi,
<br>
>>
<br>
>> I am trying to simulate a system of infinite cellulose chains
by using
<br>
>> pbc=full.
<br>
>>
<br>
>> As far as I have understood from the list this option cannot
be used
<br>
>> together with any bond constraints. Is this correct? It is
possible to
<br>
>> run simulation with the constraints, but I guess something
becomes false.
<br>
>>
<br>
>> This seems to be a problem for me, because I have a couple of
<br>
>> hydrogens that seem to get unreasonable high energy and start
<br>
>> rotating; i.e. I would like to use constraints=hbonds.
<br>
<br>
<br>
>You may use CVS version for pbc=full with lincs. SHAKE is not
<br>
>implemented yet.
<br>
<br>
Ok, I am not sure if I know what you mean with CVS version? I have
installed Gromacs 3.2.1, does that work or do I have install something
else?
<br>
<br>
/Malin
<br>
<br>
<br>
>>
<br>
>> If anyone has any suggestion about what I could do instead of
<br>
>> constraining the h-bonds, or any idea about what could
possibly be
<br>
>> wrong I would be mostly grateful.
<br>
>>
<br>
>> /Malin
<br>
>>
<br>
>> _______________________________________________
<br>
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<br>
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<br>
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>> interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
<br>
>>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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</blockquote>
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