Dear Mark,<br> <br> Thanks for your reply. I am not using both LJ and Buckingham in the same simulation, but trying to use only <span class="HOEnZb"></span> Buckingham . As my system is a polymer which is made of the monomer unit that's what i am adding to the force field. Our polymer system uses the parameters only from the residue which i have added to the forcefield through buckingham A,B & C parameters. <br>
I would like to ask the previous question again, Which values can i use for the [ pairtypes ] directive in the ffnonbonded.itp can i use arbitrary values or zeroes what i noticed from my simulations is by changing the sigma and epsilon values in the [ pairtypes ] directive energy values are changing.<br>
if i try to comment out the pairtypes 'grompp' is generating the following errors( here i am sending only one error message )<br><br>ERROR 411 [file topol.top, line 862]:<br> No default LJ-14 types<br> <br>i am a little bit confused why grompp is giving this error message though i am using the bucking potential by specifying the nbfunc as 2 in the [ default ] directive and providing the A,B,C values through [nonbond_params ] .<br>
if it is mandatory to use pair types how can i get these values for this directive.<br><br><br>Thanks in advance.<br><br><br><br><div class="gmail_quote">On Fri, Feb 24, 2012 at 12:15 PM, 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 text="#000000" bgcolor="#FFFFFF"><div class="im">
On 24/02/2012 5:20 PM, ramesh cheerla wrote:
<blockquote 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 style="width:198px;min-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></div>
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.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="im"><br>
<br>
<blockquote 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 href="mailto:Mark.Abraham@anu.edu.au" target="_blank">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>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><font color="#888888"><br>
<br>
Mark<br>
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