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.abra...@anu.edu.au
<mailto:mark.abra...@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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