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><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 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>
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<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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