Re: [gmx-users] shift the LJ potential

[Mark Abraham]

Hi,

On Mon, Oct 9, 2017 at 5:26 PM Faezeh Pousaneh  wrote:

> Hi Mark,
>
> I have a given function for pseudo hard-sphere potential,


There's no ability for GROMACS to support a true hard-sphere potential,
because for such potentials the force is always zero or undefined.

which has
> different powers than LJ and a constant. I have to insert the constant in
> order to properly define the cut-off for my hard spheres.
> I just realized that I can use "user-specified potential". I guess I can
> include the constant there, yes?
>

Yes, if anything is possible, then that's what you should do.


> One more thing, I need to have my own particles, spheres with a diameter
> "a". How can I have them in gromacs?
>

You'd need to write that code ;-)

Mark


> On Oct 9, 2017 3:44 PM, "Mark Abraham"  wrote:
>
> Hi,
>
> Shifting the potential doesn't affect the sampling - only the forces do.
> How does that affect what you're thinking of?
>
> Mark
>
> On Mon, Oct 9, 2017 at 3:14 PM Faezeh Pousaneh 
> wrote:
>
> > Hi,
> >
> > I would like to shift the LJ interaction between my particle by a
> constant,
> > (to remove attraction), how can I change the function?
> >
> >
> > 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 gmx-users-requ...@gromacs.org.
> >
> --
> 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 gmx-users-requ...@gromacs.org.
> --
> 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 gmx-users-requ...@gromacs.org.
>
-- 
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 gmx-users-requ...@gromacs.org.

Re: [gmx-users] shift the LJ potential

[Faezeh Pousaneh]

Hi Mark,

I have a given function for pseudo hard-sphere potential, which has
different powers than LJ and a constant. I have to insert the constant in
order to properly define the cut-off for my hard spheres.
I just realized that I can use "user-specified potential". I guess I can
include the constant there, yes?

One more thing, I need to have my own particles, spheres with a diameter
"a". How can I have them in gromacs?

On Oct 9, 2017 3:44 PM, "Mark Abraham"  wrote:

Hi,

Shifting the potential doesn't affect the sampling - only the forces do.
How does that affect what you're thinking of?

Mark

On Mon, Oct 9, 2017 at 3:14 PM Faezeh Pousaneh  wrote:

> Hi,
>
> I would like to shift the LJ interaction between my particle by a
constant,
> (to remove attraction), how can I change the function?
>
>
> 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 gmx-users-requ...@gromacs.org.
>
--
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 gmx-users-requ...@gromacs.org.
-- 
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 gmx-users-requ...@gromacs.org.

Re: [gmx-users] shift the LJ potential

[Mark Abraham]

Hi,

Shifting the potential doesn't affect the sampling - only the forces do.
How does that affect what you're thinking of?

Mark

On Mon, Oct 9, 2017 at 3:14 PM Faezeh Pousaneh  wrote:

> Hi,
>
> I would like to shift the LJ interaction between my particle by a constant,
> (to remove attraction), how can I change the function?
>
>
> 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 gmx-users-requ...@gromacs.org.
>
-- 
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 gmx-users-requ...@gromacs.org.

[gmx-users] shift the LJ potential

[Faezeh Pousaneh]

Hi,

I would like to shift the LJ interaction between my particle by a constant,
(to remove attraction), how can I change the function?


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 gmx-users-requ...@gromacs.org.