Re: [ESPResSo-users] Tabulated angle potential

[Tristan Bereau]

Hi Vincent,

Unfortunately I don't have enough experience with tabulated angle
potentials to help you out any further. I'll leave it to more
experienced users.

Best,
Tristan

On Mon, Aug 25, 2014 at 9:51 AM, Vincent Ustach <address@hidden> wrote:
> Hi Tristan,
>
> Thank for your response. When I use the tabulated 2-body bond potential I do
> include the scaling factor and it works just fine. I am having trouble with
> the 3-body angle potential. Last month I discussed with Axel Arnold on the
> mailing list that it might be OK to leave off the 1/r scaling factor. If I
> did include the 1/r, would you suggest I use the equilibrium bond length?
> The length to use for tabulated angles is not clear to me.
>
> Best Regards,
>
> Vincent
>
> --Vincent Ustach
>   University of California, Davis
>
>
> On Sun, Aug 24, 2014 at 11:41 PM, Tristan Bereau <address@hidden>
> wrote:
>>
>> Hi Vincent,
>>
>> It's hard to tell what exactly went wrong here, but just to point out
>> the obvious: are you aware that Espresso has a rather special way of
>> formatting the tabulated potential file? Specifically, the force is
>> rescaled by the distance:
>>
>> F(r) = -V'(r)/r
>>
>> where V'(r) is the derivative of the potential.
>>
>> Best,
>> Tristan
>>
>>
>>
>> On Mon, Aug 25, 2014 at 9:09 AM, Vincent Ustach <address@hidden>
>> wrote:
>> > Hello everyone,
>> >
>> > I am working on simulating a polymer with tabulated potentials. I
>> > noticed
>> > that the distribution of the bond angles is centered about the wrong
>> > angle,
>> > so I checked my method by comparing the built-in angle potentials-
>> > angle_cosine, angle_cossquared, and angle_harmonic with equivalent
>> > tabulated
>> > potentials. The three attached .m files creates data that I've copied
>> > into
>> > files for Espresso to read- all I do is add the header
>> >
>> > #1001 0 3.14159
>> >
>> > Attached please find the script I have used to run the simulation as
>> > well as
>> > histograms for the built-in and tabulated potentials. Each set of data
>> > represent bond angle distributions for a 100-mer (entered as an argument
>> > of
>> > the execution command).
>> >
>> > Any advice to input the tabulated potential correctly is most welcome.
>> > And
>> > sorry to attach so many files!
>> >
>> > Thank you,
>> >
>> > --Vincent Ustach
>> >
>
>