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Hi.<br>
There is an issue with constraints.<br>
H atom position is not uniquely defined with the constraints you use.<br>
Try these constraints (substitute symbols with numbers)<br>
<br>
1 2 1 rC-H<br>
1 3 1 rC-CL<br>
1 4 1 rC-CL<br>
1 5 1 rC-CL<br>
2 3 1 rH-CL<br>
2 4 1 rH-CL<br>
3 4 1 rCL-CL<br>
3 5 1 rCL-CL <br>
4 5 1 rCL-CL <br>
<br>
DD<br>
<br>
<br>
On 02/02/2011 06:20 PM, <a class="moz-txt-link-abbreviated" href="mailto:vferrario@units.it">vferrario@units.it</a> wrote:
<blockquote cite="mid:20110202172022.68102j0fg5vabhog@wmail1.units.it"
type="cite">The dynamic works, but I still have the same problems with
minimization...
<br>
<br>
<br>
"Justin A. Lemkul" <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a> ha scritto:
<br>
<br>
<blockquote type="cite"><br>
<br>
<a class="moz-txt-link-abbreviated" href="mailto:vferrario@units.it">vferrario@units.it</a> wrote:
<br>
<blockquote type="cite">Ok and which definition have you used? the
previous one with 5 atom for molecule?
<br>
<br>
</blockquote>
<br>
Yes.
<br>
<br>
-Justin
<br>
<br>
<blockquote type="cite">"Justin A. Lemkul" <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a>
ha scritto:
<br>
<br>
<blockquote type="cite"><br>
<br>
<a class="moz-txt-link-abbreviated" href="mailto:vferrario@units.it">vferrario@units.it</a> wrote:
<br>
<blockquote type="cite">Just the last thing... can you copy
your mdp file? I think I'm having some problems also with that...
Thanks.
<br>
<br>
</blockquote>
<br>
For EM, I used the .mdp file you posted in your first message and added
the line "continuation = yes." For MD, I changed nstlist from 100 to
5.
<br>
<br>
-Justin
<br>
<br>
<blockquote type="cite">Valerio
<br>
<br>
<br>
"Justin A. Lemkul" <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a> ha scritto:
<br>
<br>
<blockquote type="cite"><br>
<br>
Justin A. Lemkul wrote:
<br>
<br>
<snip>
<br>
<br>
<blockquote type="cite">I've obtained a stable trajectory
for a single CHCL3 molecule. By setting "continuation = no" (so that
constraints are not solved before step 0) in the em.mdp file, and then
reducing nstlist to 5 in md.mdp, I
<br>
</blockquote>
<br>
Ack, this should be "continuation = yes." Sorry for the confusion. I
will copy from my .mdp file...I will copy from my .mdp file... :)
<br>
<br>
-Justin
<br>
<br>
-- <br>
========================================
<br>
<br>
Justin A. Lemkul
<br>
Ph.D. Candidate
<br>
ICTAS Doctoral Scholar
<br>
MILES-IGERT Trainee
<br>
Department of Biochemistry
<br>
Virginia Tech
<br>
Blacksburg, VA
<br>
jalemkul[at]vt.edu | (540) 231-9080
<br>
<a class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>
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Justin A. Lemkul
<br>
Ph.D. Candidate
<br>
ICTAS Doctoral Scholar
<br>
MILES-IGERT Trainee
<br>
Department of Biochemistry
<br>
Virginia Tech
<br>
Blacksburg, VA
<br>
jalemkul[at]vt.edu | (540) 231-9080
<br>
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<br>
<br>
Justin A. Lemkul
<br>
Ph.D. Candidate
<br>
ICTAS Doctoral Scholar
<br>
MILES-IGERT Trainee
<br>
Department of Biochemistry
<br>
Virginia Tech
<br>
Blacksburg, VA
<br>
jalemkul[at]vt.edu | (540) 231-9080
<br>
<a class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>
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