[gmx-users] dielectric constant of water by gromacs

[Harshkumar Singh]

Can you please describe how to use pme or any other reference?


On Thu, May 29, 2014 at 3:40 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 2014-05-29 06:07, 来者可追 wrote:
>
>> Dear David,
>>    I have a problem when simulating the dielectric constant of water
>> according to g_dipoles.I used the water file in "tutor"(216 SPC waters),
>> when I write the program "g_dipoles", the result is as following, why
>> not Epsilon about 65?
>>
>> ‍=================================
>> Finite system Kirkwood g factor G_k = 0.163272
>> Infinite system Kirkwood g factor g_k = 0.123058
>>
>> Epsilon = 3.83011
>> ‍‍=================================
>>
>>
> Did you use PME? In that case it should work.
> If you used a cut-off you have to redo the simulation.
>
>
>
>>    I cannot understand " you have to give extr options, depending on how
>> you did the simulation. g_dipoles -h (hint look at the epsilonRF
>> option). If you used a cut-off then you will not get the right
>> dielectric. " (
>> https://www.mail-archive.com/gmx-users%40gromacs.org/msg18306.html ) Can
>> you explain it more for me? Thank you so much!
>> ‍‍‍‍‍‍‍
>>
>> Sincerely,
>> LiBin
>>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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-- 
Harshkumar Singh
2nd Year Integrated MSc Chemistry
IIT Bombay.