[gmx-users] Adding new residue to the the force field

[Mark Abraham]

On 24/02/2012 11:56 PM, ramesh cheerla wrote:
> Dear Mark,
>
>                  Thanks for your reply. I am not using  both  LJ and 
> Buckingham in the same simulation, but trying to use only Buckingham . 
> As my system is a polymer which is made of the monomer unit that's 
> what i am adding to the force field. Our polymer system uses the 
> parameters only from the residue  which i have added to the forcefield 
> through buckingham A,B & C parameters.
> I would like to ask the previous question again, Which values can i 
> use for the  [ pairtypes ] directive  in the ffnonbonded.itp can i use 
> arbitrary values or  zeroes what i noticed from my simulations is by 
> changing the sigma and epsilon values in the [ pairtypes ] directive 
> energy values are changing.
> if i try to comment  out the pairtypes  'grompp'  is generating the 
> following errors( here i am sending only one error message )
>
> ERROR 411 [file topol.top, line 862]:
>   No default LJ-14 types
>
> i am a little bit confused  why grompp is giving this error message 
> though i am using  the bucking potential by specifying the nbfunc as 2 
> in the [ default ] directive and providing the A,B,C values through 
> [nonbond_params ] .
> if it is mandatory to use pair types  how can i get these values for 
> this directive.

You'll have to do some detective work starting at line 862.

Mark

>
>
> Thanks in advance.
>
>
>
> On Fri, Feb 24, 2012 at 12:15 PM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 24/02/2012 5:20 PM, ramesh cheerla wrote:
>>     Dear Mark
>>                     I am very thank ful to you for your valuble
>>     suggestion. I have verified my results by changing the sigma and
>>     epsilon values in   [atomtypes ] directive of the ffnonbonded.itp
>>     . Results were uneffected by changing these values.
>>     Here i have one another doubt regarding [ pairtypes ] directive,
>>     As I am using buckingham potential for the nonbonded interactions
>>     and  have only A, B & C  values can i use zeros for the sigma and
>>     epsilon values in this directive. What i observed is results will
>>     change  by changing the sigma and epsilon values in this directive.
>>     Please suggest me how can i use correct values for the sigma and
>>     epsilon in [ pairtypes ]  directive.
>
>     As I understand things, pairs for special 1-4 interactions are not
>     used with Buckingham interactions.
>
>     Looking closer at your original post, you claim to be adding a
>     residue using Buckingham to an existing force field. No force
>     fields distributed with GROMACS use Buckingham, so if you're
>     trying to make both LJ and Buckingham work in the same simulation,
>     you will be unable to succeed.
>
>     Mark
>
>
>>
>>     Thank you in advance.
>>
>>     On Thu, Feb 23, 2012 at 7:32 AM, Mark Abraham
>>     <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>
>>         On 23/02/2012 6:02 AM, ramesh cheerla wrote:
>>
>>             Dear gromacs users,
>>
>>                                           I am adding a new residue
>>             to the existing force field in gromacs for that i am
>>             using some new atom types i added these atom types to the
>>             atomtypes.atp  file  and ffnonbonded.itp and  I am using
>>             Buckingham potential for the non-bonded interactions for
>>             that i have only A,B&C values, but in the [atomtype]
>>             directive of the ffnonbonded.itp file one has to specify
>>             the  sigma and epsilon values. How can i get these values
>>             ? or can i specify these values as zeros ?
>>
>>
>>         You will be able to use zeroes. You can verify that there's
>>         no effect by changing the values to ludicrous ones and
>>         observing that the simulation is the same.
>>
>>         Mark
>>         -- 
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>>
>
>
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