[gmx-users] Calculating Dielectric constant

[Life Sciences Inc]

So instead of using epsilon-surface = 70, I should use its value equal to 1
? By deault epsilon-surface =  0 which means it is turned off, to turn it
on one must specify a value, as mentioned in Gromacs mdp options:
"value of the relative permittivity of the imaginary surface around your
infinite system"
So what should be the value of permittivity, is there some constant value
for it? what value should I choose to simply calculate dielctric onstant? I
also did PBC correction by making my input coord whole but still simulation
is running around for 30 to 40 minutes and then stopping with Lincs error.
This means Simulation is running and parameters are correct, any
suggestions please ? as I cannot figure out what is going wrong.


Thanks a lot


On Tue, May 31, 2016 at 9:36 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 30/05/16 14:33, Life Sciences Inc wrote:
>
>> Dear ALL Gromacs users
>>
>> I am trying to calculate Dielectric constant using the option in my
>> simulation file as epsilon-surface = 70 . whenever I try to run the
>> simulaton I get this warning message
>>
>> "Since molecules/charge groups are broken using the Verlet scheme, you can
>> not use a dipole correction to the PME electrostatics."
>>
>> I am ignoring this warning by using maxwarn but after few ns simulation is
>> crashing, kindly someone tell me the solution to this problem?
>>
>> Thanks in advance
>>
>> And by the way, you have to be careful computing the dielectric constant
> using something other than 1. Please check gmx dipoles options carefully.
>
>
> --
> 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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