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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 24 07:45:23 CET 2012

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.


> 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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