By the way thank you very much for answering my questions. <br><br><div>Amit</div><div><br><div class="gmail_quote">On Tue, Sep 8, 2009 at 7:13 PM, Amit Choubey <span dir="ltr"><<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">hi,<div><br></div><div>ok the next question that bugs me is if i make a directory consisting of my modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to use pdb2gmx to get the *.top & .gro files according to the above new FF files, how do i supply this info to pdb2gmx. In other words how do i make pdb2gmx aware of the new FF files.</div>
<div><br></div><div><font color="#888888">Amit</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Tue, Sep 8, 2009 at 6:58 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
so is it a good idea to edit the original gromacs files in top directory for introducing new force field or is there a way to compliment the existing FF files by a new file made by me? <br>
</blockquote>
<br></div>
It is generally better to not mess with system-level force field files unless you're very sure of what you're doing, and experienced in making such changes. If you alter one of the original force field files, and you don't do it right, reverting the changes is often difficult. If, for example, you want to modify the OPLS-AA force field, do not ever make any changes to the original file, instead implement them in files like ffoplsaa_mod.*<br>
<br>
It is even safer to implement your changes in the local directory until you are confident everything is working properly, then if you're comfortable that you've done everything 100% right, move your files into /share/top for convenience later.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Amit<div><br>
<br>
On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Amit Choubey wrote:<br>
<br>
hi gromacs user,<br>
<br>
Is there any good way to introduce new force field in the<br>
gromacs library?<br>
<br>
<br>
Read in the manual about the organization of existing force fields,<br>
as well as the component files that are necessary to make it<br>
function. Beyond that, look at the implemented force fields<br>
themselves and see how they work together.<br>
<br>
-Justin<br>
<br>
Amit<br>
<br>
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Virginia Tech<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</blockquote></div><br></div>