Yup, that should be physically sound.
Alex
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Dear Alex, I have another question related to coulombtype selection. I dont want to use pbc in my system so, PME and Ewald are not good choices. If I use Reaction-field-zero and define a rcoulomb equal to my system size ( since epsilon-rf is 0 out of cutoff size) would it do the same work as finding epsilon-rf in generalized field reaction? THANKS! On Tue, Apr 28, 2015 at 10:22 PM, Maryam Kowsar <[email protected]> wrote: If I use PME there's no need to find epsilon-rf, but I have to change some other parameters. I will try it. Thank you very much Alex! On Tue, Apr 28, 2015 at 11:31 AM, Alex <[email protected]> wrote: With reaction-field-zero, the only option is epsilon-rf=0. That aside, if the nanotube is small, i would use cut-off electrostatics with coulomb-cutoff comparable to the length of the tube. If the tube is long, I would use standard pme. I would be extremely careful about using truncated electrostatics in general. Given the above, I am not sure I understand what's there to calculate, unless you mean running a simulation and _obtaining_ a dielectric property as a result. In that case, given you system, it is a completely different discussion. Alex MK> Not a poorly formed but a general question! MK> You are right about reaction-field-zero. reaction-field leads to MK> bad energy conservations. So, I decided to use reaction-field-zero MK> but as I have some charges I don't know what to do with them. I MK> have a CNT in which there are some ions. I want to calculate the MK> epsilon-rf for it. I don't know if epsilon-rf belongs to the whole MK> system and if so, how I should calculate it. MK> thanks! MK> On Tue, Apr 28, 2015 at 10:50 AM, Alex <[email protected]> wrote: MK> That's a pretty poorly formed question, including the part where you MK> actually "calculate" the epsilon-rf value. Can you please try again with MK> a description of your system? MK> Alex MK>> Dear all, MK>> I use reaction-field-zero as the coulombtype for my system. I wonder how I MK>> should choose the right epsilon-rf. How can I calculate the dielectric MK>> constant in the system? MK>> Thank you. -- Best regards, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. |
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