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

ramesh cheerla rameshgromacs at gmail.com
Fri Feb 24 07:20:18 CET 2012

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.

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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