Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

Thank Justin.
Mark you are right. I did not think about to check the manual. 

Thanks again.
> On 22 Jun 2017, at 15:51, Mark Abraham  wrote:
> 
> Hi,
> 
> I'd start by looking in the documentation. Section 5.3.2 of the manual
> clearly suggests putting it in the ffnonbonded.itp file, which is where you
> expected to find it at the start of this thread, right? :-)
> 
> Mark
> 
> On Thu, Jun 22, 2017 at 3:47 PM gozde ergin  > wrote:
> 
>> Hey Justin,
>> 
>> I figured out how they calculated the sigma values.
>> Basically they just take the geometric mean of nitrogen and oxygen sigma
>> and epsilon from ffnonbed.itp file in OPLS-AA force field
>> and calculated the pairwise LJ for N-O interaction.
>> 
>> Now I also try to add this information in my topol.top file.
>> In order to do that as you have mentioned I added a section ,
>> 
>> [ nonbond_params ]
>> ; i j   funcsigma   epsilon
>> opls_287  opls_272  1  0.323161248385416  0.790543521382599
>> 
>> 
>> after [ atoms ] section however I am facing with an error :
>> 
>> Fatal error:
>> Syntax error - File topol.top, line 42
>> Last line read:
>> '[ nonbond_params ]'
>> Invalid order for directive nonbond_params
>> 
>> Any suggestion would be appreciated.
>> 
>>> On 21 Jun 2017, at 16:46, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 6/21/17 10:39 AM, gozde ergin wrote:
 Hi MArk,
 Thanks for the respond. I understood that point however I still do not
>> get which sigma to change.
 I the paper JCTC 2017, Miller et. al. they have mentioned that they
>> increase the for nitrogen–carboxylate oxygen interactions in OPLSAA.
 However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
>> notrogen and one for carboxylate oxygen.
 
>>   sigmaepsilon
 opls_287   N3   7  14.00670-0.300   A3.25000e-01
>> 7.11280e-01
 opls_272   O2   8  15.99940-0.800   A2.96000e-01
>> 8.78640e-01
 Which one defines the amino nitrogen–carboxylate oxygen interactions?
 Which sigma should I change?
>>> 
>>> What people are doing more and more is introducing pair-specific
>> parameters to override the combination rule values.  That's likely what is
>> being referred to. OPLS-AA by default does not use pair-specific LJ
>> interactions, hence why you find no [nonbond_params] in ffnonbonded.itp.
>> The same is true of AMBER.  CHARMM uses some (also called NBFIX in the
>> literature), while GROMOS uses a ton of these.
>>> 
>>> To override the LJ combination rules, add a [nonbond_params] directive
>> with the published parameters, which refer to an *interaction*, not an atom
>> type.
>>> 
>>> -Justin
>>> 
 Thanks
> On 21 Jun 2017, at 16:21, Mark Abraham 
>> wrote:
> 
> Hi,
> 
> Different force fields work differently and thus are implemented
> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
>> sigma
> is a property of the atomtype
> 
> Mark
> 
> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin 
>> wrote:
> 
>> Dear users,
>> 
>> I am trying to change the sigma value of amino nitrogen–carboxylate
>> oxygen
>> interactions in OPLSAA in GROMACS.
>> However I have difficulties to understand which parameter i should
>> change
>> in ffnonbonded.itp file?
>> I am looking something like [ nonbond_params ] section however it is
>> not
>> exist in ffnonbonded.itp?
>> Any help would be appreciated.
>> 
>> Thanks in advance.
>> --
>> 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!
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> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
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>>> 
>>> --
>>> ==
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> 
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>> 
>>> jalem...@outerbanks.umaryland.edu 
>>>  > jalem...@outerbanks.umaryland.edu 
>> 

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Mark Abraham]

Hi,

I'd start by looking in the documentation. Section 5.3.2 of the manual
clearly suggests putting it in the ffnonbonded.itp file, which is where you
expected to find it at the start of this thread, right? :-)

Mark

On Thu, Jun 22, 2017 at 3:47 PM gozde ergin  wrote:

> Hey Justin,
>
> I figured out how they calculated the sigma values.
> Basically they just take the geometric mean of nitrogen and oxygen sigma
> and epsilon from ffnonbed.itp file in OPLS-AA force field
> and calculated the pairwise LJ for N-O interaction.
>
> Now I also try to add this information in my topol.top file.
> In order to do that as you have mentioned I added a section ,
>
> [ nonbond_params ]
> ; i j   funcsigma   epsilon
> opls_287  opls_272  1  0.323161248385416  0.790543521382599
>
>
> after [ atoms ] section however I am facing with an error :
>
> Fatal error:
> Syntax error - File topol.top, line 42
> Last line read:
> '[ nonbond_params ]'
> Invalid order for directive nonbond_params
>
> Any suggestion would be appreciated.
>
> > On 21 Jun 2017, at 16:46, Justin Lemkul  wrote:
> >
> >
> >
> > On 6/21/17 10:39 AM, gozde ergin wrote:
> >> Hi MArk,
> >> Thanks for the respond. I understood that point however I still do not
> get which sigma to change.
> >> I the paper JCTC 2017, Miller et. al. they have mentioned that they
> increase the for nitrogen–carboxylate oxygen interactions in OPLSAA.
> >> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
> notrogen and one for carboxylate oxygen.
> >>
>sigmaepsilon
> >>  opls_287   N3   7  14.00670-0.300   A3.25000e-01
> 7.11280e-01
> >>  opls_272   O2   8  15.99940-0.800   A2.96000e-01
> 8.78640e-01
> >> Which one defines the amino nitrogen–carboxylate oxygen interactions?
> >> Which sigma should I change?
> >
> > What people are doing more and more is introducing pair-specific
> parameters to override the combination rule values.  That's likely what is
> being referred to. OPLS-AA by default does not use pair-specific LJ
> interactions, hence why you find no [nonbond_params] in ffnonbonded.itp.
> The same is true of AMBER.  CHARMM uses some (also called NBFIX in the
> literature), while GROMOS uses a ton of these.
> >
> > To override the LJ combination rules, add a [nonbond_params] directive
> with the published parameters, which refer to an *interaction*, not an atom
> type.
> >
> > -Justin
> >
> >> Thanks
> >>> On 21 Jun 2017, at 16:21, Mark Abraham 
> wrote:
> >>>
> >>> Hi,
> >>>
> >>> Different force fields work differently and thus are implemented
> >>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
> sigma
> >>> is a property of the atomtype
> >>>
> >>> Mark
> >>>
> >>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin 
> wrote:
> >>>
>  Dear users,
> 
>  I am trying to change the sigma value of amino nitrogen–carboxylate
> oxygen
>  interactions in OPLSAA in GROMACS.
>  However I have difficulties to understand which parameter i should
> change
>  in ffnonbonded.itp file?
>  I am looking something like [ nonbond_params ] section however it is
> not
>  exist in ffnonbonded.itp?
>  Any help would be appreciated.
> 
>  Thanks in advance.
>  --
>  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
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> >>> --
> >>> 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
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> send a mail to gmx-users-requ...@gromacs.org.
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu  jalem...@outerbanks.umaryland.edu> | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul <
> http://mackerell.umaryland.edu/~jalemkul>
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List <
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before
> 

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Justin Lemkul]

On 6/22/17 9:47 AM, gozde ergin wrote:

Hey Justin,

I figured out how they calculated the sigma values.
Basically they just take the geometric mean of nitrogen and oxygen sigma and 
epsilon from ffnonbed.itp file in OPLS-AA force field
and calculated the pairwise LJ for N-O interaction.

Now I also try to add this information in my topol.top file.
In order to do that as you have mentioned I added a section ,

[ nonbond_params ]
; i j   funcsigma   epsilon
opls_287  opls_272  1  0.323161248385416  0.790543521382599


after [ atoms ] section however I am facing with an error :

Fatal error:
Syntax error - File topol.top, line 42
Last line read:
'[ nonbond_params ]'
Invalid order for directive nonbond_params

Any suggestion would be appreciated.



You can't declare force field parameters after you've introduced a 
[moleculetype].  Put it in ffnonbonded.itp or immediately after the #include 
statement for the force field.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

Hey Justin,

I figured out how they calculated the sigma values. 
Basically they just take the geometric mean of nitrogen and oxygen sigma and 
epsilon from ffnonbed.itp file in OPLS-AA force field 
and calculated the pairwise LJ for N-O interaction.

Now I also try to add this information in my topol.top file. 
In order to do that as you have mentioned I added a section ,

[ nonbond_params ]
; i j   funcsigma   epsilon
opls_287  opls_272  1  0.323161248385416  0.790543521382599


after [ atoms ] section however I am facing with an error :

Fatal error:
Syntax error - File topol.top, line 42
Last line read:
'[ nonbond_params ]'
Invalid order for directive nonbond_params

Any suggestion would be appreciated.

> On 21 Jun 2017, at 16:46, Justin Lemkul  wrote:
> 
> 
> 
> On 6/21/17 10:39 AM, gozde ergin wrote:
>> Hi MArk,
>> Thanks for the respond. I understood that point however I still do not get 
>> which sigma to change.
>> I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
>> the for nitrogen–carboxylate oxygen interactions in OPLSAA.
>> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino 
>> notrogen and one for carboxylate oxygen.
>>  
>>  sigmaepsilon
>>  opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
>>  opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01
>> Which one defines the amino nitrogen–carboxylate oxygen interactions?
>> Which sigma should I change?
> 
> What people are doing more and more is introducing pair-specific parameters 
> to override the combination rule values.  That's likely what is being 
> referred to. OPLS-AA by default does not use pair-specific LJ interactions, 
> hence why you find no [nonbond_params] in ffnonbonded.itp.  The same is true 
> of AMBER.  CHARMM uses some (also called NBFIX in the literature), while 
> GROMOS uses a ton of these.
> 
> To override the LJ combination rules, add a [nonbond_params] directive with 
> the published parameters, which refer to an *interaction*, not an atom type.
> 
> -Justin
> 
>> Thanks
>>> On 21 Jun 2017, at 16:21, Mark Abraham  wrote:
>>> 
>>> Hi,
>>> 
>>> Different force fields work differently and thus are implemented
>>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
>>> is a property of the atomtype
>>> 
>>> Mark
>>> 
>>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:
>>> 
 Dear users,
 
 I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
 interactions in OPLSAA in GROMACS.
 However I have difficulties to understand which parameter i should change
 in ffnonbonded.itp file?
 I am looking something like [ nonbond_params ] section however it is not
 exist in ffnonbonded.itp?
 Any help would be appreciated.
 
 Thanks in advance.
 --
 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.
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu  
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> 
> 
> ==
> -- 
> Gromacs Users mailing list
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> * Please search the archive at 
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>  before posting!
> 
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> 
> 
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>  or send 
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> 

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Justin Lemkul]

On 6/21/17 10:55 AM, gozde ergin wrote:

However in the paper they have mentioned that they increased the sigma  for 
amino nitrogen–carboxylate oxygen interactions
by 0.13Angstrom   relative to the original value.
So I assume there should be original value?
However you mentioned that there is no pair-specific LJ interaction in OPLSAA.
Even if I add a [nonbond_params] what epsilon and sigma should I use? Because 
they talk about the increment in sigma and I do not know the original value.
Maybe I should connect them directly.



Yes, do that to make sure they're consistent with the publication, but 
combination rules are explained in the PDF manual (and presumably in the 
original literature for the force field!) so you can calculate these very 
easily.  It's simple arithmetic.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

However in the paper they have mentioned that they increased the sigma  for 
amino nitrogen–carboxylate oxygen interactions 
by 0.13Angstrom   relative to the original value.
So I assume there should be original value? 
However you mentioned that there is no pair-specific LJ interaction in OPLSAA. 
Even if I add a [nonbond_params] what epsilon and sigma should I use? Because 
they talk about the increment in sigma and I do not know the original value.
Maybe I should connect them directly.

Thanks Justin.

> On 21 Jun 2017, at 16:46, Justin Lemkul  wrote:
> 
> 
> 
> On 6/21/17 10:39 AM, gozde ergin wrote:
>> Hi MArk,
>> Thanks for the respond. I understood that point however I still do not get 
>> which sigma to change.
>> I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
>> the for nitrogen–carboxylate oxygen interactions in OPLSAA.
>> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino 
>> notrogen and one for carboxylate oxygen.
>>  
>>  sigmaepsilon
>>  opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
>>  opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01
>> Which one defines the amino nitrogen–carboxylate oxygen interactions?
>> Which sigma should I change?
> 
> What people are doing more and more is introducing pair-specific parameters 
> to override the combination rule values.  That's likely what is being 
> referred to. OPLS-AA by default does not use pair-specific LJ interactions, 
> hence why you find no [nonbond_params] in ffnonbonded.itp.  The same is true 
> of AMBER.  CHARMM uses some (also called NBFIX in the literature), while 
> GROMOS uses a ton of these.
> 
> To override the LJ combination rules, add a [nonbond_params] directive with 
> the published parameters, which refer to an *interaction*, not an atom type.
> 
> -Justin
> 
>> Thanks
>>> On 21 Jun 2017, at 16:21, Mark Abraham  wrote:
>>> 
>>> Hi,
>>> 
>>> Different force fields work differently and thus are implemented
>>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
>>> is a property of the atomtype
>>> 
>>> Mark
>>> 
>>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:
>>> 
 Dear users,
 
 I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
 interactions in OPLSAA in GROMACS.
 However I have difficulties to understand which parameter i should change
 in ffnonbonded.itp file?
 I am looking something like [ nonbond_params ] section however it is not
 exist in ffnonbonded.itp?
 Any help would be appreciated.
 
 Thanks in advance.
 --
 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.
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Justin Lemkul]

On 6/21/17 10:39 AM, gozde ergin wrote:

Hi MArk,

Thanks for the respond. I understood that point however I still do not get 
which sigma to change.
I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
the for nitrogen–carboxylate oxygen interactions in OPLSAA.
However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino notrogen 
and one for carboxylate oxygen.

   
sigmaepsilon
  opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
  opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01

Which one defines the amino nitrogen–carboxylate oxygen interactions?
Which sigma should I change?



What people are doing more and more is introducing pair-specific parameters to 
override the combination rule values.  That's likely what is being referred to. 
OPLS-AA by default does not use pair-specific LJ interactions, hence why you 
find no [nonbond_params] in ffnonbonded.itp.  The same is true of AMBER.  CHARMM 
uses some (also called NBFIX in the literature), while GROMOS uses a ton of these.


To override the LJ combination rules, add a [nonbond_params] directive with the 
published parameters, which refer to an *interaction*, not an atom type.


-Justin


Thanks

On 21 Jun 2017, at 16:21, Mark Abraham  wrote:

Hi,

Different force fields work differently and thus are implemented
differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
is a property of the atomtype

Mark

On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:


Dear users,

I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
interactions in OPLSAA in GROMACS.
However I have difficulties to understand which parameter i should change
in ffnonbonded.itp file?
I am looking something like [ nonbond_params ] section however it is not
exist in ffnonbonded.itp?
Any help would be appreciated.

Thanks in advance.
--
Gromacs Users mailing list

* Please search the archive at
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==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

Hi MArk,

Thanks for the respond. I understood that point however I still do not get 
which sigma to change.
I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
the for nitrogen–carboxylate oxygen interactions in OPLSAA.
However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino notrogen 
and one for carboxylate oxygen.

  
sigmaepsilon
 opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
 opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01

Which one defines the amino nitrogen–carboxylate oxygen interactions?
Which sigma should I change?

Thanks
> On 21 Jun 2017, at 16:21, Mark Abraham  wrote:
> 
> Hi,
> 
> Different force fields work differently and thus are implemented
> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
> is a property of the atomtype
> 
> Mark
> 
> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:
> 
>> Dear users,
>> 
>> I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
>> interactions in OPLSAA in GROMACS.
>> However I have difficulties to understand which parameter i should change
>> in ffnonbonded.itp file?
>> I am looking something like [ nonbond_params ] section however it is not
>> exist in ffnonbonded.itp?
>> Any help would be appreciated.
>> 
>> Thanks in advance.
>> --
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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Mark Abraham]

Hi,

Different force fields work differently and thus are implemented
differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
is a property of the atomtype

Mark

On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:

> Dear users,
>
> I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
> interactions in OPLSAA in GROMACS.
> However I have difficulties to understand which parameter i should change
> in ffnonbonded.itp file?
> I am looking something like [ nonbond_params ] section however it is not
> exist in ffnonbonded.itp?
> Any help would be appreciated.
>
> Thanks in advance.
> --
> Gromacs Users mailing list
>
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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