Choice of thermostat during MD for cavity

Dear all,

I want to run molecular dynamics only for a relatively small “cavity” inside the system, keeping all the environment fixed. What thermostat should be used for this model?

Thank you in advance,
Dmitrii

Hi Dimitrii,

what do you mean by ‘keeping all the environment fixed’? Do plan to restrain/freeze it or do you want the thermostat to act only on that part of the system, and not on the “cavity”?

I would say that in both cases the choiche of the thermostat is not that influent; I guess it depends on your specific system, but a-priori there should not be any reason why v-rescale should not work, for example. What you may want to do , on the other hand, is to thermostat each groups differently: it could be beneficial to use different coupling times for the group representing the environment and the one representing the “cavity” (eventually -1 for the latter).

But that of course depends on the specific system; what are you aiming to simulate?