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

[ramesh cheerla]

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.


Thanks in advance.



On Fri, Feb 24, 2012 at 12:15 PM, Mark Abraham <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>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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