[gmx-users] 回复： g_dielectric errors for getting frequency dependent dielectric constants

[来者可追]

Dear David,
      Thanks for your reply.
       I have other questions when  calculating frequency dependent dielectric constants through g_dielectric.

1. After using " g_dipoles -corr mol " command to get the dipcorr.xvg, if I uesd " g_dielectric " program, the error is as following.
================
Fatal error:
nparm = 0 in file expfit.c, line 465
========================if I used " g_dielectric -eint 50 -bfit 5 -efit 100 -ffn exp ", then the error is:
================
nbegin = 50, x[nbegin] = 5, tbegin = 5
Step       chi^2      Lambda          A1          A2          A3
Segmentation Fault================

2. When I read the manul about g_dielectric, I have a question about the output file " epsw.xvg ". In the manul, it discribs " The second file contains the real and imaginary parts of the frequency-dependent dielectric constant ". How can I get the real parts of the frequency-dependent dielectric constant only ? ( just like the fig. 2. the frequency dependence of the dielectric constant in your papaer  J. Chem. Phys. 108 (1998) pp. 10220-10230  ) 

 I appreciate your help. Thanks a lot!




------------------ 原始邮件 ------------------
发件人: "spoel";<spoel at xray.bmc.uu.se>;
发送时间: 2014年5月30日(星期五) 下午2:11
收件人: "gmx-users"<gmx-users at gromacs.org>; 

主题: Re: [gmx-users] dielectric constant of water by gromacs



On 2014-05-30 07:39, Harshkumar Singh wrote:
> Can you please describe how to use pme or any other reference?
coulombtype = PME
in your mdp file.

>
>
> 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
>> --
>> Gromacs Users mailing list
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>
>
>


-- 
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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