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On 14/11/2010 2:42 AM, Junqiao Lee wrote:
<blockquote
cite="mid:AANLkTik6uXqpAWuC8VD+cKXGizQGvwoYa6K8BFhR0mJz@mail.gmail.com"
type="cite">
<div>Running the simulation in NVT doesn't seem to work too.</div>
<div> </div>
<div><span lang="EN-AU">And (other than the system not blowing up
now) similar to the NPT simulations, both 2CosZ*Vel-X and
1/Viscosity that I've got out of the test runs were 0.</span></div>
</blockquote>
<br>
Is the starting configuration stable under normal MD?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTik6uXqpAWuC8VD+cKXGizQGvwoYa6K8BFhR0mJz@mail.gmail.com"
type="cite">
<div><span lang="EN-AU"></span> </div>
<div>On Sat, Nov 13, 2010 at 11:17 PM, Junqiao Lee <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:aeondrift@gmail.com">aeondrift@gmail.com</a>></span>
wrote:<br>
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<div class="gmail_quote">
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204,
204, 204);">
<div>Hi,</div>
<div> </div>
<div>I've tried running an NEMD run in NPT vis setting the "<span
lang="EN-AU">cos_acceleration = 0.3" parameter to
determine the solvent viscosity.</span></div>
<div><span lang="EN-AU">However my system kept spectacularly
exploding.</span></div>
<div><span lang="EN-AU"></span> </div>
<div><span lang="EN-AU">I've also tried running with the
acc_grps specified for 7 molecules (out of the 250 within
the system), but it still didn't work.</span></div>
<div><span lang="EN-AU"></span> </div>
<div><span lang="EN-AU">cos_acceleration = ~0.3 nm ps^-2 seem
like a reasonable value to use?</span></div>
<div><span lang="EN-AU"><br>
Am I only restricted to running NEMD calcs. in NVT?</span></div>
<div><span lang="EN-AU"></span> </div>
<div><span lang="EN-AU">Thanks for the help.</span></div>
<div><span lang="EN-AU"></span> </div>
<div><span lang="EN-AU">Cheers,</span></div>
<div><span lang="EN-AU">Junqiao LEE (Wade)</span></div>
<font color="#888888">
<div><span lang="EN-AU">Curtin University<br>
Dept. of Chem. [NRI]</span></div>
</font></blockquote>
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