<div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Hello,<br>
I am trying to prepare the input files for an MD run. After running grompp,<br>
I received the following note:<br>
<br>
NOTE 1 [file npt.mdp, line unknown]:<br>
The Berendsen thermostat does not generate the correct kinetic energy<br>
distribution. You might want to consider using the V-rescale thermostat.<br>
<br>
How reliable this note is? </blockquote><div><br>It's true.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">And how can I implement V-rescale thermostat in y<br>
input file (I found nothing in the manual).</blockquote><div><br>Substitute "berendsen" with "V-rescale" in the mdp file. <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Also, when I changed the thermostat to nose-hoover, it said that it can not<br>
be used with Berendsen barostat. Why?<br>
<br>
</blockquote></div>C'est la vie...<br><br clear="all"><br>-- <br>Vitaly V. Chaban, Ph.D. (ABD)<br>School of Chemistry<br>V.N. Karazin Kharkiv National University<br>Svoboda sq.,4, Kharkiv 61077, Ukraine<br>email: <a href="mailto:chaban@univer.kharkov.ua">chaban@univer.kharkov.ua</a>,<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a><br>
skype: vvchaban, mob.: +38-097-8259698 <br><a href="http://www-rmn.univer.kharkov.ua/chaban.html">http://www-rmn.univer.kharkov.ua/chaban.html</a><br>===================================<br>!!! Looking for a postdoctoral position !!!<br>
===================================<br>