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On 24/02/2012 11:56 PM, ramesh cheerla wrote:
<blockquote
cite="mid:CAPNFZqdLUWu5BeQX3pMNm=Cq3wfw_qXR-g-mqkVNO_M+6VinWg@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
You'll have to do some detective work starting at line 862.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPNFZqdLUWu5BeQX3pMNm=Cq3wfw_qXR-g-mqkVNO_M+6VinWg@mail.gmail.com"
type="cite"><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 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 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
moz-do-not-send="true"
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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