Re: [gmx-users] Lennard Jones parameters

[Justin Lemkul]

On 5/28/13 1:01 AM, Ishwor wrote:

Dear all
I want to study the simulation of Carbonmonoxide in water. I have seen the
Lennard Jones parameters, force constant and partial charges of water in the
file spce.itp inherent in gromacs but couldnt get the parameters for CO .I
will be pleased if anyone provide me the LJ parameters (epsilon and sigma)
,partial charge of Carbon Monoxide.Due to some technical diffculties I have
got no access for the published papers.  Thanks



Having access to the literature will be essential for continuing your work.  In 
any case, doing such a simulation is not as simple as "give me the parameters 
for molecule X."  You need to choose a parent force field that will represent 
your system and obtain or derive compatible parameters.  Parameterization is no 
easy task (although a diatomic molecule should be fairly straightforward), and 
you need to be very familiar with how the chosen force field works and is 
derived, information that will require thorough examination of the literature.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Lennard-Jones Parameters

[Peter C. Lai]

On 2012-10-15 05:54:58AM -0400, Justin Lemkul wrote:
> 
> 
> On 10/15/12 5:45 AM, cuong nguyen wrote:
> > Dear,
> >
> > The top file downloaded from PRODRG did not consist of [atomtypes]. Please
> > tell me how can I add and use this function?
> >
> 
> I see no need to change anything about the L-J parameters.  Is there some 
> reason 
> you believe them to be incorrect?  If you modify L-J parameters, you're no 
> longer using Gromos96 43a1.  In PRODRG topologies, the charges and charge 
> groups 
> certainly need changing, but I have never seen a need to hack the L-J 
> parameters.
> 
> -Justin

I think he needs to go back and ask the authors of the paper he is trying to 
reproduce about how to parameterize 1-octanol according their specifications. 
If they are using different LJ for the atoms in this molecule from 43a1 then 
they are obviously not using gromos96 43a1 :)

> 
> > Best regards,
> >
> > Cuong
> >
> > On 15 October 2012 16:43, Peter C. Lai  wrote:
> >
> >> Is there no [atomtypes] section in the top file?
> >>
> >> On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
> >>> Thanks for you email.
> >>> I already had the .gro and .top files from PRODRG. Now I want to
> >> reproduce
> >>> these files following the LJ parameters in a published paper (charge,
> >> sigma
> >>> and epsilon values). I can change the charge in the top file, yet I do
> >> not
> >>> know how to change sigma and epsilon values.
> >>>
> >>> Best regards,
> >>>
> >>> Cuong
> >>>
> >>> On 15 October 2012 13:57, Peter C. Lai  wrote:
> >>>
>  It's hard to understand your question. What do you mean by "reference
>  parameters"? You said you already obtained a .gro and .top from PRODRG,
>  which
>  uses the gromos 43a1 forcefield to derive the parameters, so if you
> >> need
>  to change the LJ parameters, edit the top file it gave you.
> 
>  If you want to reproduce the results of a published paper, you should
> >> use
>  the
>  forcefield and parameters specified in that paper and contact the
> >> author(s)
>  if more details are needed.
> 
>  On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> > Thank you very much for your email, Justin.
> > in case I want to use the reference parameters, which force-field and
>  what
> > should I do to get the .gro and .top files for this molecule?
> >
> > Best regards,
> >
> > Cuong
> >
> >
> > On 12 October 2012 21:14, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 10/12/12 8:04 AM, cuong nguyen wrote:
> >>
> >>>Dear Gromacs Users,
> >>>
> >>> I got the .gro and .top files of 1-octanol downloaded from PRODRG
>  website.
> >>> Please let me know if I can change charge, epsilon and sigma of
> >> the
> >>> molecule as written in a paper? and How to do?
> >>>
> >>>
> >> Atom types from PRODRG rarely, if ever, need changing.  Charges
> >> can be
> >> taken first by chemical homology (group-based approach that makes
>  Gromos
> >> force fields convenient) and then by calculating the charges
> >> yourself.
>    For
> >> 1-octanol, it should be very straightforward to obtain parameters,
> >> zero
> >> charges on all the C atoms except for the one in the alocohol, then
> >> standard alcohol charges for the C-O-H.  Whether or not those
>  parameters
> >> are sufficiently accurate is up to you to decide, but that's the
>  approach
> >> one would take with this particular force field.
> >>
> >> -Justin
> >>
> >> --
> >> ==**==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Research Scientist
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>
> >> ==**==
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>  http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >> * Please search the archive at http://www.gromacs.org/**
> >> Support/Mailing_Lists/Search<
>  http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
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> >> interface or send it to gmx-users-requ...@gromacs.org.
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> >>
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Re: [gmx-users] Lennard-Jones Parameters

[Justin Lemkul]

On 10/15/12 5:45 AM, cuong nguyen wrote:

Dear,

The top file downloaded from PRODRG did not consist of [atomtypes]. Please
tell me how can I add and use this function?



I see no need to change anything about the L-J parameters.  Is there some reason 
you believe them to be incorrect?  If you modify L-J parameters, you're no 
longer using Gromos96 43a1.  In PRODRG topologies, the charges and charge groups 
certainly need changing, but I have never seen a need to hack the L-J parameters.


-Justin


Best regards,

Cuong

On 15 October 2012 16:43, Peter C. Lai  wrote:


Is there no [atomtypes] section in the top file?

On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:

Thanks for you email.
I already had the .gro and .top files from PRODRG. Now I want to

reproduce

these files following the LJ parameters in a published paper (charge,

sigma

and epsilon values). I can change the charge in the top file, yet I do

not

know how to change sigma and epsilon values.

Best regards,

Cuong

On 15 October 2012 13:57, Peter C. Lai  wrote:


It's hard to understand your question. What do you mean by "reference
parameters"? You said you already obtained a .gro and .top from PRODRG,
which
uses the gromos 43a1 forcefield to derive the parameters, so if you

need

to change the LJ parameters, edit the top file it gave you.

If you want to reproduce the results of a published paper, you should

use

the
forcefield and parameters specified in that paper and contact the

author(s)

if more details are needed.

On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:

Thank you very much for your email, Justin.
in case I want to use the reference parameters, which force-field and

what

should I do to get the .gro and .top files for this molecule?

Best regards,

Cuong


On 12 October 2012 21:14, Justin Lemkul  wrote:




On 10/12/12 8:04 AM, cuong nguyen wrote:


   Dear Gromacs Users,

I got the .gro and .top files of 1-octanol downloaded from PRODRG

website.

Please let me know if I can change charge, epsilon and sigma of

the

molecule as written in a paper? and How to do?



Atom types from PRODRG rarely, if ever, need changing.  Charges

can be

taken first by chemical homology (group-based approach that makes

Gromos

force fields convenient) and then by calculating the charges

yourself.

  For

1-octanol, it should be very straightforward to obtain parameters,

zero

charges on all the C atoms except for the one in the alocohol, then
standard alcohol charges for the C-O-H.  Whether or not those

parameters

are sufficiently accurate is up to you to decide, but that's the

approach

one would take with this particular force field.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>


==**==
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==
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu | Birmingham AL 35294-4461
(205) 690-0808|
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Re: [gmx-users] Lennard-Jones Parameters

[cuong nguyen]

Dear,

The top file downloaded from PRODRG did not consist of [atomtypes]. Please
tell me how can I add and use this function?

Best regards,

Cuong

On 15 October 2012 16:43, Peter C. Lai  wrote:

> Is there no [atomtypes] section in the top file?
>
> On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
> > Thanks for you email.
> > I already had the .gro and .top files from PRODRG. Now I want to
> reproduce
> > these files following the LJ parameters in a published paper (charge,
> sigma
> > and epsilon values). I can change the charge in the top file, yet I do
> not
> > know how to change sigma and epsilon values.
> >
> > Best regards,
> >
> > Cuong
> >
> > On 15 October 2012 13:57, Peter C. Lai  wrote:
> >
> > > It's hard to understand your question. What do you mean by "reference
> > > parameters"? You said you already obtained a .gro and .top from PRODRG,
> > > which
> > > uses the gromos 43a1 forcefield to derive the parameters, so if you
> need
> > > to change the LJ parameters, edit the top file it gave you.
> > >
> > > If you want to reproduce the results of a published paper, you should
> use
> > > the
> > > forcefield and parameters specified in that paper and contact the
> author(s)
> > > if more details are needed.
> > >
> > > On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> > > > Thank you very much for your email, Justin.
> > > > in case I want to use the reference parameters, which force-field and
> > > what
> > > > should I do to get the .gro and .top files for this molecule?
> > > >
> > > > Best regards,
> > > >
> > > > Cuong
> > > >
> > > >
> > > > On 12 October 2012 21:14, Justin Lemkul  wrote:
> > > >
> > > > >
> > > > >
> > > > > On 10/12/12 8:04 AM, cuong nguyen wrote:
> > > > >
> > > > >>   Dear Gromacs Users,
> > > > >>
> > > > >> I got the .gro and .top files of 1-octanol downloaded from PRODRG
> > > website.
> > > > >> Please let me know if I can change charge, epsilon and sigma of
> the
> > > > >> molecule as written in a paper? and How to do?
> > > > >>
> > > > >>
> > > > > Atom types from PRODRG rarely, if ever, need changing.  Charges
> can be
> > > > > taken first by chemical homology (group-based approach that makes
> > > Gromos
> > > > > force fields convenient) and then by calculating the charges
> yourself.
> > >  For
> > > > > 1-octanol, it should be very straightforward to obtain parameters,
> zero
> > > > > charges on all the C atoms except for the one in the alocohol, then
> > > > > standard alcohol charges for the C-O-H.  Whether or not those
> > > parameters
> > > > > are sufficiently accurate is up to you to decide, but that's the
> > > approach
> > > > > one would take with this particular force field.
> > > > >
> > > > > -Justin
> > > > >
> > > > > --
> > > > > ==**==
> > > > >
> > > > > Justin A. Lemkul, Ph.D.
> > > > > Research Scientist
> > > > > Department of Biochemistry
> > > > > Virginia Tech
> > > > > Blacksburg, VA
> > > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > > > >
> > > > > ==**==
> > > > > --
> > > > > gmx-users mailing listgmx-users@gromacs.org
> > > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > > > * Please search the archive at http://www.gromacs.org/**
> > > > > Support/Mailing_Lists/Search<
> > > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > > > > * Please don't post (un)subscribe requests to the list. Use the www
> > > > > interface or send it to gmx-users-requ...@gromacs.org.
> > > > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > > http://www.gromacs.org/Support/Mailing_Lists>
> > > > >
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > --
> > > ==
> > > Peter C. Lai| University of Alabama-Birmingham
> > > Programmer/Analyst  | KAUL 752A
> > > Genetics, Div. of Research  | 705 South 20th Street
> > > p...@uab.edu | Birmingham AL 35294-4461
> > > (205) 690-0808|
> > > ==
> > >
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
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> > > * Please search the archive at
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Re: [gmx-users] Lennard-Jones Parameters

[Peter C. Lai]

Is there no [atomtypes] section in the top file?

On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
> Thanks for you email.
> I already had the .gro and .top files from PRODRG. Now I want to reproduce
> these files following the LJ parameters in a published paper (charge, sigma
> and epsilon values). I can change the charge in the top file, yet I do not
> know how to change sigma and epsilon values.
> 
> Best regards,
> 
> Cuong
> 
> On 15 October 2012 13:57, Peter C. Lai  wrote:
> 
> > It's hard to understand your question. What do you mean by "reference
> > parameters"? You said you already obtained a .gro and .top from PRODRG,
> > which
> > uses the gromos 43a1 forcefield to derive the parameters, so if you need
> > to change the LJ parameters, edit the top file it gave you.
> >
> > If you want to reproduce the results of a published paper, you should use
> > the
> > forcefield and parameters specified in that paper and contact the author(s)
> > if more details are needed.
> >
> > On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> > > Thank you very much for your email, Justin.
> > > in case I want to use the reference parameters, which force-field and
> > what
> > > should I do to get the .gro and .top files for this molecule?
> > >
> > > Best regards,
> > >
> > > Cuong
> > >
> > >
> > > On 12 October 2012 21:14, Justin Lemkul  wrote:
> > >
> > > >
> > > >
> > > > On 10/12/12 8:04 AM, cuong nguyen wrote:
> > > >
> > > >>   Dear Gromacs Users,
> > > >>
> > > >> I got the .gro and .top files of 1-octanol downloaded from PRODRG
> > website.
> > > >> Please let me know if I can change charge, epsilon and sigma of the
> > > >> molecule as written in a paper? and How to do?
> > > >>
> > > >>
> > > > Atom types from PRODRG rarely, if ever, need changing.  Charges can be
> > > > taken first by chemical homology (group-based approach that makes
> > Gromos
> > > > force fields convenient) and then by calculating the charges yourself.
> >  For
> > > > 1-octanol, it should be very straightforward to obtain parameters, zero
> > > > charges on all the C atoms except for the one in the alocohol, then
> > > > standard alcohol charges for the C-O-H.  Whether or not those
> > parameters
> > > > are sufficiently accurate is up to you to decide, but that's the
> > approach
> > > > one would take with this particular force field.
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==**==
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Research Scientist
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > > >
> > > > ==**==
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > > * Please search the archive at http://www.gromacs.org/**
> > > > Support/Mailing_Lists/Search<
> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > > > * Please don't post (un)subscribe requests to the list. Use the www
> > > > interface or send it to gmx-users-requ...@gromacs.org.
> > > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > http://www.gromacs.org/Support/Mailing_Lists>
> > > >
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > --
> > ==
> > Peter C. Lai| University of Alabama-Birmingham
> > Programmer/Analyst  | KAUL 752A
> > Genetics, Div. of Research  | 705 South 20th Street
> > p...@uab.edu | Birmingham AL 35294-4461
> > (205) 690-0808|
> > ==
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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> -- 
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> * Please do

Re: [gmx-users] Lennard-Jones Parameters

[cuong nguyen]

Thanks for you email.
I already had the .gro and .top files from PRODRG. Now I want to reproduce
these files following the LJ parameters in a published paper (charge, sigma
and epsilon values). I can change the charge in the top file, yet I do not
know how to change sigma and epsilon values.

Best regards,

Cuong

On 15 October 2012 13:57, Peter C. Lai  wrote:

> It's hard to understand your question. What do you mean by "reference
> parameters"? You said you already obtained a .gro and .top from PRODRG,
> which
> uses the gromos 43a1 forcefield to derive the parameters, so if you need
> to change the LJ parameters, edit the top file it gave you.
>
> If you want to reproduce the results of a published paper, you should use
> the
> forcefield and parameters specified in that paper and contact the author(s)
> if more details are needed.
>
> On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> > Thank you very much for your email, Justin.
> > in case I want to use the reference parameters, which force-field and
> what
> > should I do to get the .gro and .top files for this molecule?
> >
> > Best regards,
> >
> > Cuong
> >
> >
> > On 12 October 2012 21:14, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 10/12/12 8:04 AM, cuong nguyen wrote:
> > >
> > >>   Dear Gromacs Users,
> > >>
> > >> I got the .gro and .top files of 1-octanol downloaded from PRODRG
> website.
> > >> Please let me know if I can change charge, epsilon and sigma of the
> > >> molecule as written in a paper? and How to do?
> > >>
> > >>
> > > Atom types from PRODRG rarely, if ever, need changing.  Charges can be
> > > taken first by chemical homology (group-based approach that makes
> Gromos
> > > force fields convenient) and then by calculating the charges yourself.
>  For
> > > 1-octanol, it should be very straightforward to obtain parameters, zero
> > > charges on all the C atoms except for the one in the alocohol, then
> > > standard alcohol charges for the C-O-H.  Whether or not those
> parameters
> > > are sufficiently accurate is up to you to decide, but that's the
> approach
> > > one would take with this particular force field.
> > >
> > > -Justin
> > >
> > > --
> > > ==**==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Research Scientist
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
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Re: [gmx-users] Lennard-Jones Parameters

[Peter C. Lai]

It's hard to understand your question. What do you mean by "reference
parameters"? You said you already obtained a .gro and .top from PRODRG, which 
uses the gromos 43a1 forcefield to derive the parameters, so if you need
to change the LJ parameters, edit the top file it gave you.

If you want to reproduce the results of a published paper, you should use the 
forcefield and parameters specified in that paper and contact the author(s)
if more details are needed.

On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> Thank you very much for your email, Justin.
> in case I want to use the reference parameters, which force-field and what
> should I do to get the .gro and .top files for this molecule?
> 
> Best regards,
> 
> Cuong
> 
> 
> On 12 October 2012 21:14, Justin Lemkul  wrote:
> 
> >
> >
> > On 10/12/12 8:04 AM, cuong nguyen wrote:
> >
> >>   Dear Gromacs Users,
> >>
> >> I got the .gro and .top files of 1-octanol downloaded from PRODRG website.
> >> Please let me know if I can change charge, epsilon and sigma of the
> >> molecule as written in a paper? and How to do?
> >>
> >>
> > Atom types from PRODRG rarely, if ever, need changing.  Charges can be
> > taken first by chemical homology (group-based approach that makes Gromos
> > force fields convenient) and then by calculating the charges yourself.  For
> > 1-octanol, it should be very straightforward to obtain parameters, zero
> > charges on all the C atoms except for the one in the alocohol, then
> > standard alcohol charges for the C-O-H.  Whether or not those parameters
> > are sufficiently accurate is up to you to decide, but that's the approach
> > one would take with this particular force field.
> >
> > -Justin
> >
> > --
> > ==**==
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
> >
> > ==**==
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Re: [gmx-users] Lennard-Jones Parameters

[cuong nguyen]

Thank you very much for your email, Justin.
in case I want to use the reference parameters, which force-field and what
should I do to get the .gro and .top files for this molecule?

Best regards,

Cuong


On 12 October 2012 21:14, Justin Lemkul  wrote:

>
>
> On 10/12/12 8:04 AM, cuong nguyen wrote:
>
>>   Dear Gromacs Users,
>>
>> I got the .gro and .top files of 1-octanol downloaded from PRODRG website.
>> Please let me know if I can change charge, epsilon and sigma of the
>> molecule as written in a paper? and How to do?
>>
>>
> Atom types from PRODRG rarely, if ever, need changing.  Charges can be
> taken first by chemical homology (group-based approach that makes Gromos
> force fields convenient) and then by calculating the charges yourself.  For
> 1-octanol, it should be very straightforward to obtain parameters, zero
> charges on all the C atoms except for the one in the alocohol, then
> standard alcohol charges for the C-O-H.  Whether or not those parameters
> are sufficiently accurate is up to you to decide, but that's the approach
> one would take with this particular force field.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] Lennard-Jones Parameters

[Justin Lemkul]

On 10/12/12 8:04 AM, cuong nguyen wrote:

  Dear Gromacs Users,

I got the .gro and .top files of 1-octanol downloaded from PRODRG website.
Please let me know if I can change charge, epsilon and sigma of the
molecule as written in a paper? and How to do?



Atom types from PRODRG rarely, if ever, need changing.  Charges can be taken 
first by chemical homology (group-based approach that makes Gromos force fields 
convenient) and then by calculating the charges yourself.  For 1-octanol, it 
should be very straightforward to obtain parameters, zero charges on all the C 
atoms except for the one in the alocohol, then standard alcohol charges for the 
C-O-H.  Whether or not those parameters are sufficiently accurate is up to you 
to decide, but that's the approach one would take with this particular force field.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

[lloyd riggs]

A quick answer to this is, there's two sets of tables based on equations I know 
of off hand for LJ's and calculating the other such LJ parameters from these.  
In one it uses the epsilon/ sigma and the other a table of either the 9-6 or 
the 6-12.  The later two you can look up either on the European or US standards 
data base on the web or in a CRC book.  The former, you have to do a 
conversion, although for your force field you might have to do a back 
conversion if you look up say the 6-12.  I would trust A professor more with 
this though...and getting the proper equations.  With the equation you have 
listed below it would be strait forward plug and paste and then a 
calculator...either you have one or the other portions of the equation.  I 
assume the 4 epsilon is from the normal equation, and the sigma as well for a 
12-6 equation.  All of these are on wiki though as well.

Hope thats not too confusing.

Stephan Watkins

 Original-Nachricht 
> Datum: Mon, 20 Feb 2012 17:36:07 + (GMT)
> Von: Lara Bunte 
> An: "gmx-users@gromacs.org" 
> Betreff: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

> 
> 
> Hello
> I use a charmm force field in gromacs. I almost finished my
> parametrization except for Lennard-Jones parameters. For this parameters I 
> want to adopt
> the values in the charmm force field for the basic atom types. 
> 
> In gromacs I have to put this parameters in the ffnonbonded.itp file in
> the section [ pairtypes ] and I have to give following informations: 
> 
> ; i j   func    sigma1-4    epsilon1-4 ;
> THESE ARE 1-4 INTERACTIONS
> 
> in example
> 
> CP1 CP1 1   0.338541512893  0.04184
> 
> Now here is a section of information given in the charmm documentation. 
> 
> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
> !
> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
> !
> !atom  ignoredepsilon  Rmin/2   ignored  
> eps,1-4   Rmin/2,1-4
> !
> HN1  0.0   -0.04600.2245 
> HN2  0.0   -0.04600.2245 
> 
> 
> The question is: 
> 
> 
> How to adopt the values in the charmm force field for the basic atom types
> in gromacs? I do not really know what I have to write in the [ pairtypes ]
> section in gromacs. 
> 
> 
> Thank you for helping me
> Greetings
> Lara
> 
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Re: [gmx-users] Lennard-Jones Parameters in ffnonbonded.itp

[Mark Abraham]

On 21/02/2012 4:36 AM, Lara Bunte wrote:


Hello
I use a charmm force field in gromacs. I almost finished my parametrization 
except for Lennard-Jones parameters. For this parameters I want to adopt the 
values in the charmm force field for the basic atom types.

In gromacs I have to put this parameters in the ffnonbonded.itp file in the 
section [ pairtypes ] and I have to give following informations:

; i j   funcsigma1-4epsilon1-4 ; THESE ARE 1-4 INTERACTIONS

in example

CP1 CP1 1   0.338541512893  0.04184

Now here is a section of information given in the charmm documentation.

!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom  ignoredepsilon  Rmin/2   ignored   eps,1-4   Rmin/2,1-4
!
HN1  0.0   -0.04600.2245
HN2  0.0   -0.04600.2245


Sometimes CHARMM has special values for 1-4 interactions of some atom 
types (in the last two columns) and sometimes not. CHARMM computes the 
actual interaction parameters in the program. GROMACS has pre-computed 
these in the [ pairtypes ] according to the combination rule. IIRC 
there's some redundant entries where neither atom type has special 1-4 
interactions. See manual 4.1.1 and 5.3.2 for how GROMACS needs these 
computations to work.





The question is:


How to adopt the values in the charmm force field for the basic atom types in 
gromacs? I do not really know what I have to write in the [ pairtypes ] section 
in gromacs.


What's wrong with the existing contents of 
$GMXLIB/share/top/charmm27.ff/ffnonbonded.itp?


Mark
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Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

[Mark Abraham]

Darrell Koskinen wrote:

Hi Mark,
I thought opls_127 and opls_128 were the representative atoms to use for 
ammonia. Please correct me if I am wrong.


I don't know anything more than what's in ffoplsa* files or the papers.

Would the adsorption of the polar ammonia molecule onto the polar 
(hydrogen-terminated) edges of the graphene sheet be affected by the 
missing LJ parameter on the H atoms?


Define "missing". If it is zero by design, that's because zero served 
the purpose during the parameterization, and the documentation as quoted 
by you is perhaps erroneous with respect to small molecules. If it 
oplsa_128 should have non-zero LJ then you'll need to find more evidence 
of that in the OPLSAA papers, or by consulting the authors. Note that 
most models of water do not have LJ on the H atoms, and so not having LJ 
on H atoms of solvated ammonia is probably quite consistent.


Doesn't this bring us back to the point of quite a while ago, that an 
ammonia model that was probably not parameterized for the gas phase 
might not be useful in the gas phase?


Mark


Date: Mon, 26 Oct 2009 08:47:14 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users 
Message-ID: <4ae4c762.2060...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Justin A. Lemkul wrote:
 

Darrell Koskinen wrote:
   
I looked through the ffoplsaanb.itp file and see that all the H 
atoms except for the following four have zero LJ parameters:


HC OPLS_140 alkane H
HA OPLS_146 Benzene H
H4 OPLS_345 Cytosine H-C6
H5 OPLS_355 Adenine & Guanine H-C2

However, in the paper "Development and Testing of the OPLS All-Atom 
Force Field on Conformational Energetics and Properties of Organic 
Liquids", it states: "The original OPLS (optimized potentials for 
liquid simulations) potential functions used a partially united-atom 
(UA) model; sites for nonbonded interactions are placed on all 
nonhydrogen atoms and on hydrogens attached to heteroatoms or 
carbons in aromatic rings". Later, the paper indicates that the 
paramters were adopted as much as possible from the OPLS-UA force 
field. Thus, since "sites for nonbonded interactions are placed on 
hydrogens attached to heteroatoms ", it appears to me that a site 
for a non-bonded interaction should exist on the H atoms within 
ammonia. Is my interpretation incorrect?


  
I don't think so.  Each of the above examples you've cited above is 
for a C-H bond in an aromatic ring.  In OPLS, all N-H bonds involved 
hydrogen atoms with zero LJ parameters.  See, for example, any 
backbone NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will 
see the atom types used.



I think you're both partly wrong. Type 140 is not for C-H in an 
aromatic ring, and if you grep 1.008 ffoplsaanb.itp you get many more 
H atom types with LJ. Certainly Justin's right inasmuch as amide N-H 
type 241 has no H LJ parameters. Perhaps there's other text that 
Darrell hasn't found yet, or backbone nitrogen is not considered a 
heteroatom :-).


Mark

 

Darrell
 

Date: Mon, 19 Oct 2009 19:07:22 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users 
Message-ID: <4adc1e3a.8010...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Darrell Koskinen wrote:
 
   

Hi,
I see that the Lennard Jones parameters for the N & H atoms in 
ammonia, represented by opls_127 and opls_128 in the file 
ffoplsaanb.itp are:


opls_127   NT  7 14.00670-1.020   A3.42000e-01  
7.11280e-01
opls_128   H   1   1.00800 0.340   A0.0e+00  
0.0e+00


Why are sigma and epsilon both zero for H? Are the LJ parameters 
for H embedded in the parameter for NT? If so, how were these 
parameters combined?
  
What do other H have? What do the OPLS-AA paper(s) have to say 
about such H atoms?


Mark


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Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

[Mark Abraham]

Justin A. Lemkul wrote:



Darrell Koskinen wrote:
I looked through the ffoplsaanb.itp file and see that all the H atoms 
except for the following four have zero LJ parameters:


HC OPLS_140 alkane H
HA OPLS_146 Benzene H
H4 OPLS_345 Cytosine H-C6
H5 OPLS_355 Adenine & Guanine H-C2

However, in the paper "Development and Testing of the OPLS All-Atom 
Force Field on Conformational Energetics and Properties of Organic 
Liquids", it states: "The original OPLS (optimized potentials for 
liquid simulations) potential functions used a partially united-atom 
(UA) model; sites for nonbonded interactions are placed on all 
nonhydrogen atoms and on hydrogens attached to heteroatoms or carbons 
in aromatic rings". Later, the paper indicates that the paramters were 
adopted as much as possible from the OPLS-UA force field. Thus, since 
"sites for nonbonded interactions are placed on hydrogens attached to 
heteroatoms ", it appears to me that a site for a non-bonded 
interaction should exist on the H atoms within ammonia. Is my 
interpretation incorrect?




I don't think so.  Each of the above examples you've cited above is for 
a C-H bond in an aromatic ring.  In OPLS, all N-H bonds involved 
hydrogen atoms with zero LJ parameters.  See, for example, any backbone 
NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will see the atom 
types used.


I think you're both partly wrong. Type 140 is not for C-H in an aromatic 
ring, and if you grep 1.008 ffoplsaanb.itp you get many more H atom 
types with LJ. Certainly Justin's right inasmuch as amide N-H type 241 
has no H LJ parameters. Perhaps there's other text that Darrell hasn't 
found yet, or backbone nitrogen is not considered a heteroatom :-).


Mark


Darrell

Date: Mon, 19 Oct 2009 19:07:22 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users 
Message-ID: <4adc1e3a.8010...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Darrell Koskinen wrote:
 

Hi,
I see that the Lennard Jones parameters for the N & H atoms in 
ammonia, represented by opls_127 and opls_128 in the file 
ffoplsaanb.itp are:


opls_127   NT  7 14.00670-1.020   A3.42000e-01  
7.11280e-01
opls_128   H   1   1.00800 0.340   A0.0e+00  
0.0e+00


Why are sigma and epsilon both zero for H? Are the LJ parameters for 
H embedded in the parameter for NT? If so, how were these parameters 
combined?



What do other H have? What do the OPLS-AA paper(s) have to say about 
such H atoms?


Mark
  

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Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

[Justin A. Lemkul]

Darrell Koskinen wrote:
I looked through the ffoplsaanb.itp file and see that all the H atoms 
except for the following four have zero LJ parameters:


HC OPLS_140 alkane H
HA OPLS_146 Benzene H
H4 OPLS_345 Cytosine H-C6
H5 OPLS_355 Adenine & Guanine H-C2

However, in the paper "Development and Testing of the OPLS All-Atom 
Force Field on Conformational Energetics and Properties of Organic 
Liquids", it states: "The original OPLS (optimized potentials for liquid 
simulations) potential functions used a partially united-atom (UA) 
model; sites for nonbonded interactions are placed on all nonhydrogen 
atoms and on hydrogens attached to heteroatoms or carbons in aromatic 
rings". Later, the paper indicates that the paramters were adopted as 
much as possible from the OPLS-UA force field. Thus, since "sites for 
nonbonded interactions are placed on hydrogens attached to heteroatoms 
", it appears to me that a site for a non-bonded interaction should 
exist on the H atoms within ammonia. Is my interpretation incorrect?




I don't think so.  Each of the above examples you've cited above is for a C-H 
bond in an aromatic ring.  In OPLS, all N-H bonds involved hydrogen atoms with 
zero LJ parameters.  See, for example, any backbone NH, amide (ASN/GLN), or 
amine (LYS/LYSH), etc and you will see the atom types used.


-Justin


Thanks.

Darrell

Date: Mon, 19 Oct 2009 19:07:22 +1100
From: Mark Abraham 
Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in
ffoplsaa
To: Discussion list for GROMACS users 
Message-ID: <4adc1e3a.8010...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Darrell Koskinen wrote:
 

Hi,
I see that the Lennard Jones parameters for the N & H atoms in 
ammonia, represented by opls_127 and opls_128 in the file 
ffoplsaanb.itp are:


opls_127   NT  7 14.00670-1.020   A3.42000e-01  
7.11280e-01
opls_128   H   1   1.00800 0.340   A0.0e+00  
0.0e+00


Why are sigma and epsilon both zero for H? Are the LJ parameters for 
H embedded in the parameter for NT? If so, how were these parameters 
combined?



What do other H have? What do the OPLS-AA paper(s) have to say about 
such H atoms?


Mark
  

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

[Mark Abraham]

Darrell Koskinen wrote:

Hi,
I see that the Lennard Jones parameters for the N & H atoms in ammonia, 
represented by opls_127 and opls_128 in the file ffoplsaanb.itp are:


opls_127   NT  7 14.00670-1.020   A3.42000e-01  7.11280e-01
opls_128   H   1   1.00800 0.340   A0.0e+00  
0.0e+00


Why are sigma and epsilon both zero for H? Are the LJ parameters for H 
embedded in the parameter for NT? If so, how were these parameters 
combined?


What do other H have? What do the OPLS-AA paper(s) have to say about 
such H atoms?


Mark
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