Re: [gmx-users] Fwd: shift the LJ potential

2017-10-11 Thread Faezeh Pousaneh 
I see, thanks Mark,


Best regards


On Wed, Oct 11, 2017 at 3:46 PM, Mark Abraham 
wrote:

> Hi,
>
> To reproduce the training data for each forcefield, e.g. some experimental
> or other computational result, e.g. the density of argon gas under various
> conditions. Details of what and how do vary with the force field, are are
> documented in its literature, of course.
>
> Mark
>
> On Wed, Oct 11, 2017 at 3:43 PM Faezeh Pousaneh 
> wrote:
>
>> Apart from my own simulation, I do no understand how the values of C6 and
>> C12 are obtained for each atoms in ''atometypes'' in force fields, could
>> you tell me?
>>
>>
>> Best regards
>>
>>
>> On Wed, Oct 11, 2017 at 3:06 PM, Wes Barnett 
>> wrote:
>>
>>>
>>>
>>> On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh 
>>> wrote:
>>>
 Thank you Wes and Mark,

 Wes, that is what I am trying to do. However, still have problem.
 I do not know how to derive sigma, epsilon (or C6 and C12) for my
 particle?
 How the force fields have obtained C6 and C12 values in their .itp
 files for each atom?

>>>
>>> That depends on what the purpose of your simulation is. If you're just
>>> wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units
>>> could be reasonable.
>>>
>>>


 Best regards


 On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett 
 wrote:

> On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh 
> wrote:
>
> > 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?
> > .
> >
>
> This should get you started in generating your own tables:
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>
> If all you're looking to do is create repulsive spheres (again, not
> true
> hard spheres as Mark said; just removing attractions from the
> interactions), then cut off your interactions at 2^(1/6)*sigma and
> shift
> the potential at the cutoff to zero in your table. If you want
> different
> size spheres you need to subtract an additional term from r in the
> denominators of the c6 and c12 terms.
>
> --
> James "Wes" Barnett
> Postdoctoral Research Scientist
> Department of Chemical Engineering
> Kumar Research Group 
> Columbia University
> w.barn...@columbia.edu
> http://wbarnett.us
> --
> 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.
>


>>>
>>>
>>> --
>>> James "Wes" Barnett
>>> Postdoctoral Research Scientist
>>> Department of Chemical Engineering
>>> Kumar Research Group 
>>> Columbia University
>>> w.barn...@columbia.edu
>>> http://wbarnett.us
>>>
>>
>>
-- 
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] Fwd: shift the LJ potential

2017-10-11 Thread Mark Abraham 
Hi,

To reproduce the training data for each forcefield, e.g. some experimental
or other computational result, e.g. the density of argon gas under various
conditions. Details of what and how do vary with the force field, are are
documented in its literature, of course.

Mark

On Wed, Oct 11, 2017 at 3:43 PM Faezeh Pousaneh  wrote:

> Apart from my own simulation, I do no understand how the values of C6 and
> C12 are obtained for each atoms in ''atometypes'' in force fields, could
> you tell me?
>
>
> Best regards
>
>
> On Wed, Oct 11, 2017 at 3:06 PM, Wes Barnett 
> wrote:
>
>>
>>
>> On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh 
>> wrote:
>>
>>> Thank you Wes and Mark,
>>>
>>> Wes, that is what I am trying to do. However, still have problem.
>>> I do not know how to derive sigma, epsilon (or C6 and C12) for my
>>> particle?
>>> How the force fields have obtained C6 and C12 values in their .itp files
>>> for each atom?
>>>
>>
>> That depends on what the purpose of your simulation is. If you're just
>> wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units
>> could be reasonable.
>>
>>
>>>
>>>
>>> Best regards
>>>
>>>
>>> On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett 
>>> wrote:
>>>
 On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh 
 wrote:

 > 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?
 > .
 >

 This should get you started in generating your own tables:
 http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

 If all you're looking to do is create repulsive spheres (again, not true
 hard spheres as Mark said; just removing attractions from the
 interactions), then cut off your interactions at 2^(1/6)*sigma and shift
 the potential at the cutoff to zero in your table. If you want different
 size spheres you need to subtract an additional term from r in the
 denominators of the c6 and c12 terms.

 --
 James "Wes" Barnett
 Postdoctoral Research Scientist
 Department of Chemical Engineering
 Kumar Research Group 
 Columbia University
 w.barn...@columbia.edu
 http://wbarnett.us
 --
 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.

>>>
>>>
>>
>>
>> --
>> James "Wes" Barnett
>> Postdoctoral Research Scientist
>> Department of Chemical Engineering
>> Kumar Research Group 
>> Columbia University
>> w.barn...@columbia.edu
>> http://wbarnett.us
>>
>
>
-- 
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] Fwd: shift the LJ potential

2017-10-11 Thread Faezeh Pousaneh 
Apart from my own simulation, I do no understand how the values of C6 and
C12 are obtained for each atoms in ''atometypes'' in force fields, could
you tell me?


Best regards


On Wed, Oct 11, 2017 at 3:06 PM, Wes Barnett  wrote:

>
>
> On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh 
> wrote:
>
>> Thank you Wes and Mark,
>>
>> Wes, that is what I am trying to do. However, still have problem.
>> I do not know how to derive sigma, epsilon (or C6 and C12) for my
>> particle?
>> How the force fields have obtained C6 and C12 values in their .itp files
>> for each atom?
>>
>
> That depends on what the purpose of your simulation is. If you're just
> wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units
> could be reasonable.
>
>
>>
>>
>> Best regards
>>
>>
>> On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett 
>> wrote:
>>
>>> On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh 
>>> wrote:
>>>
>>> > 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?
>>> > .
>>> >
>>>
>>> This should get you started in generating your own tables:
>>> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>>>
>>> If all you're looking to do is create repulsive spheres (again, not true
>>> hard spheres as Mark said; just removing attractions from the
>>> interactions), then cut off your interactions at 2^(1/6)*sigma and shift
>>> the potential at the cutoff to zero in your table. If you want different
>>> size spheres you need to subtract an additional term from r in the
>>> denominators of the c6 and c12 terms.
>>>
>>> --
>>> James "Wes" Barnett
>>> Postdoctoral Research Scientist
>>> Department of Chemical Engineering
>>> Kumar Research Group 
>>> Columbia University
>>> w.barn...@columbia.edu
>>> http://wbarnett.us
>>> --
>>> 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.
>>>
>>
>>
>
>
> --
> James "Wes" Barnett
> Postdoctoral Research Scientist
> Department of Chemical Engineering
> Kumar Research Group 
> Columbia University
> w.barn...@columbia.edu
> http://wbarnett.us
>
-- 
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] Fwd: shift the LJ potential

2017-10-11 Thread Wes Barnett 
On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh 
wrote:

> Thank you Wes and Mark,
>
> Wes, that is what I am trying to do. However, still have problem.
> I do not know how to derive sigma, epsilon (or C6 and C12) for my particle?
> How the force fields have obtained C6 and C12 values in their .itp files
> for each atom?
>

That depends on what the purpose of your simulation is. If you're just
wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units
could be reasonable.


>
>
> Best regards
>
>
> On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett 
> wrote:
>
>> On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh 
>> wrote:
>>
>> > 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?
>> > .
>> >
>>
>> This should get you started in generating your own tables:
>> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>>
>> If all you're looking to do is create repulsive spheres (again, not true
>> hard spheres as Mark said; just removing attractions from the
>> interactions), then cut off your interactions at 2^(1/6)*sigma and shift
>> the potential at the cutoff to zero in your table. If you want different
>> size spheres you need to subtract an additional term from r in the
>> denominators of the c6 and c12 terms.
>>
>> --
>> James "Wes" Barnett
>> Postdoctoral Research Scientist
>> Department of Chemical Engineering
>> Kumar Research Group 
>> Columbia University
>> w.barn...@columbia.edu
>> http://wbarnett.us
>> --
>> 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.
>>
>
>


-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
-- 
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] Fwd: shift the LJ potential

2017-10-11 Thread Faezeh Pousaneh 
Thank you Wes and Mark,

Wes, that is what I am trying to do. However, still have problem.
I do not know how to derive sigma, epsilon (or C6 and C12) for my particle?
How the force fields have obtained C6 and C12 values in their .itp files
for each atom?


Best regards


On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett  wrote:

> On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh 
> wrote:
>
> > 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?
> > .
> >
>
> This should get you started in generating your own tables:
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
>
> If all you're looking to do is create repulsive spheres (again, not true
> hard spheres as Mark said; just removing attractions from the
> interactions), then cut off your interactions at 2^(1/6)*sigma and shift
> the potential at the cutoff to zero in your table. If you want different
> size spheres you need to subtract an additional term from r in the
> denominators of the c6 and c12 terms.
>
> --
> James "Wes" Barnett
> Postdoctoral Research Scientist
> Department of Chemical Engineering
> Kumar Research Group 
> Columbia University
> w.barn...@columbia.edu
> http://wbarnett.us
> --
> 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] Fwd: shift the LJ potential

2017-10-10 Thread Wes Barnett 
On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh 
wrote:

> 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?
> .
>

This should get you started in generating your own tables:
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

If all you're looking to do is create repulsive spheres (again, not true
hard spheres as Mark said; just removing attractions from the
interactions), then cut off your interactions at 2^(1/6)*sigma and shift
the potential at the cutoff to zero in your table. If you want different
size spheres you need to subtract an additional term from r in the
denominators of the c6 and c12 terms.

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
-- 
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] Fwd: shift the LJ potential

2017-10-10 Thread 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.