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On 24/02/2012 5:20 PM, ramesh cheerla wrote:
<blockquote
cite="mid:CAPNFZqfH+a9kkO9G+MuJP+VESYU1QUCqoPQWqzGVS9ukfWBXDg@mail.gmail.com"
type="cite">Dear Mark <br>
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.<br>
Here i have one another doubt regarding [ pairtypes ] directive,
As I am using <span class="img A"
style="width:198px;height:65px;margin-top:12px;margin-right:5px">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 </span>sigma and epsilon values in this directive.<br>
Please suggest me how can i use correct values for the sigma and
epsilon in [ pairtypes ] directive.<br>
</blockquote>
<br>
As I understand things, pairs for special 1-4 interactions are not
used with Buckingham interactions.<br>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPNFZqfH+a9kkO9G+MuJP+VESYU1QUCqoPQWqzGVS9ukfWBXDg@mail.gmail.com"
type="cite"><br>
Thank you in advance.<br>
<br>
<div class="gmail_quote">On Thu, Feb 23, 2012 at 7:32 AM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="im">On 23/02/2012 6:02 AM, ramesh cheerla wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Dear gromacs users,<br>
<br>
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 ?<br>
</blockquote>
<br>
</div>
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.<span class="HOEnZb"><font
color="#888888"><br>
<br>
Mark<br>
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