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On 29/03/2012 8:22 PM, Hendry wrote:
<blockquote
cite="mid:CANDSGMHY=sY47yjr4B+Hpnja0k4ompwHaAJG_O9DWWyXjaZBAw@mail.gmail.com"
type="cite">
<p class="MsoNormal"><span style="font-family:"Times New
Roman","serif"" lang="EN-US">Hi,</span></p>
<p class="MsoNormal" style="text-indent:24.0pt"><span
style="font-family:"Times New
Roman","serif"" lang="EN-US"> </span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-family:"Times New
Roman","serif"" lang="EN-US">I am using Gromacs
4.5.4. After successful minimization by SD, I continued with
equilibration step but I got the below errors. I tried many
times with different parameters but the problem still
persists. I have given errors and md parameters of
equilibration step below. I have also provided my minimization
output at the end. Could you provide some suggestions what
went wrong?. </span></p>
</blockquote>
<br>
You are using PR-pressure coupling for equilibration, which is an
unstable combination. You are coupling ions to their own thermostat,
which is unstable. Do check out the GROMACS manual for discussion of
how these algorithms work, and also the website for some practical
observations.<br>
<br>
Mark<br>
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