Dear Prof. Thomas and Chase,<div><br></div><div>I have a little confuse about the tag MD/THERMOSTAT/DEFINE_REGION. If some atoms are not listed in the region does it mean those atom are just simply follow the the Newtonian EOM?. In addition, what is the meaning of setting DEFINED in the tag MD/THERMOSTAT/REGION?<br><br></div><div>Regards</div><div>Nam</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday, 6 January 2020 at 11:19:24 pm UTC+11 tkuehne wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div style="word-wrap:break-word">Nope, this has nothing to do with that, it is to specifies to how many <div>degrees of freedom the thermostat is coupled. If I recall it correctly </div><div>GLOBAL means 3 DOF of the whole system and MASSIVE to all </div><div>3N DOF. MOLECULE should be 3 per molecule, which for a QS </div><div>calculations, where a molecule is identical to an atom shouldn’t be </div><div>much different from MASSIVE. I personally don’t see any reason for </div><div>GLOBAL anymore and always use MASSIVE and control if I would </div><div>like to access dynamic or mere static equilibrium properties via the </div><div>corresponding time constant. </div><div><br></div><div>Cheers, </div><div>Thomas</div><div><div><br><div><div><blockquote type="cite"></blockquote></div></div></div></div></div><div style="word-wrap:break-word"><div><div><div><div><blockquote type="cite"><div>Am 06.01.2020 um 11:42 schrieb MD Simulation <<a href data-email-masked rel="nofollow">mdsi...@gmail.com</a>>:</div><br></blockquote></div></div></div></div></div><div style="word-wrap:break-word"><div><div><div><div><blockquote type="cite"><div><div dir="ltr">Thanks Thomas!<div><br></div><div>What setting would I use for MD/THERMOSTAT/REGION? Would it still be GLOBAL or would it be MOLECULE?<br><div><br>On Monday, January 6, 2020 at 4:56:14 AM UTC-5, tkuehne wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Dear Chase, <div><br></div><div>IMHO there are two ways to do that: </div><div>(i) use THERMOSTAT/DEFINE_REGION to thermostat your surface. However, in that </div><div>case you have to specify SUBSYS/VELOCITIES to assign the velocities of your </div><div>molecule by hand or restarting them … </div><div>(ii) Use MD/THERMAL_REGION/DEFINE_REGION, to define the surface AND your </div><div>molecule, as well as their respective temeratures. However, this way you can only </div><div>specify LAGEVIN for the surface and NVE for the molecule, which should be good enough. </div><div><br></div><div>Cheers, </div><div>Thomas</div><div><br><div><blockquote type="cite"><div>Am 05.01.2020 um 16:50 schrieb MD Simulation <<a rel="nofollow">mdsi...@gmail.com</a>>:</div><br><div><div dir="ltr">Hi,<div><br></div><div>I need to run a simulation of a molecule being shot at a surface. I'd like to do two things: 1) thermostat the surface and 2) assign a specific velocity to the small molecule.</div><div><br></div><div>I see in the MD/THERMOSTAT section, there is a keyword REGION...is this what I would want to do?</div><div><br></div><div>If anyone has some ideas, I would appreciate it! </div><div><br></div><div>Thanks for the help,</div><div>Chase</div></div><div><br></div>
-- <br>
You received this message because you are subscribed to the Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving emails from it, send an email to <a rel="nofollow">c...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/998e7f97-6653-43fd-ac2a-5d0bb9f0b8fd%40googlegroups.com?utm_medium=email&utm_source=footer" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en-AU&q=https://groups.google.com/d/msgid/cp2k/998e7f97-6653-43fd-ac2a-5d0bb9f0b8fd%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1599570602820000&usg=AFQjCNFkzFlVkvE7NtEP9StWLnwYwuC14A">https://groups.google.com/d/msgid/cp2k/998e7f97-6653-43fd-ac2a-5d0bb9f0b8fd%40googlegroups.com</a>.<br>
</div></blockquote></div><br></div><br><br><div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">==============================</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Thomas D. Kühne</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Dynamics of Condensed Matter</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Chair of Theoretical Chemistry</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">University of Paderborn</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Warburger Str. 100</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">D-33098 Paderborn</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Germany</div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><a rel="nofollow">td...@mail.upb.de</a></div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><a href="tel:+49%205251%20605726" value="+495251605726" target="_blank" rel="nofollow">+49/(0)5251/60-5726</a></div></div></div></div>
</div>
<br></div></blockquote></div></div></div><div><br></div>
-- <br>
You received this message because you are subscribed to the Google Groups "cp2k" group.<br></div></blockquote></div></div></div></div></div><div style="word-wrap:break-word"><div><div><div><div><blockquote type="cite"><div>
To unsubscribe from this group and stop receiving emails from it, send an email to <a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/bc337ca7-c204-4681-a894-b0cc99ddc4ad%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en-AU&q=https://groups.google.com/d/msgid/cp2k/bc337ca7-c204-4681-a894-b0cc99ddc4ad%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1599570602824000&usg=AFQjCNEgmqB0fRvVl1yLMtGlDtdHgdH65w">https://groups.google.com/d/msgid/cp2k/bc337ca7-c204-4681-a894-b0cc99ddc4ad%40googlegroups.com</a>.<br>
</div></blockquote></div><br></div></div></div></div><div style="word-wrap:break-word"><br><br><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">==============================</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Thomas D. Kühne</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Dynamics of Condensed Matter</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Chair of Theoretical Chemistry</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">University of Paderborn</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Warburger Str. 100</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">D-33098 Paderborn</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Germany</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><a href data-email-masked rel="nofollow">td...@mail.upb.de</a></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><a href="tel:+49%205251%20605726" value="+495251605726" target="_blank" rel="nofollow">+49/(0)5251/60-5726</a></div></div></div></div>
</div>
<br></div></blockquote></div>