<div>Hi Pablo,</div>
<div> </div>
<div>I would write .rtp entries and so on for each monomer. </div>
<div> </div>
<div>You copy the modified files into your working directory.</div>
<div> </div>
<div>Have a great day,</div>
<div>Andrea<br><br></div>
<div class="gmail_quote">2009/10/6 Englebienne, P. <span dir="ltr"><<a href="mailto:P.Englebienne@tue.nl">P.Englebienne@tue.nl</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
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<p><font face="Arial" size="2"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hi all,</span></font></p>
<p><font face="Arial" size="2"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"> </span></font></p>
<p><font face="Arial" size="2"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">I’m looking to perform simulations on a series of synthetic co-polymers containing a variety of building blocks. I will be testing different sequences of the monomers, therefore I am looking for a way to streamline the generation of the topologies.</span></font></p>
<p><font face="Arial" size="2"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"> </span></font></p>
<p><font face="Arial" size="2"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">I have been reading Chapter 5 of the manual, but I’m still a bit puzzled about how to proceed to build topologies for my system. Should I make an .itp file for each monomer? Or generate .rtp, .hdb, .tdb and .atp files for all the possible monomers I will be using? In the case of the latter, how can I direct GROMACS to read a local copy of the databases instead of a global one?</span></font></p>
<p><font face="Arial" size="2"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"> </span></font></p>
<p><font face="Arial" size="2"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">I’ll appreciate any pointers in this direction.</span></font></p>
<p><font face="Arial" size="2"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"> </span></font></p>
<p><font face="Arial" size="2"><span style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Thanks!</span></font></p>
<p><font face="Arial" size="2"><span lang="EN" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">--<br>Pablo Englebienne, PhD<br>Institute of Complex Molecular Systems (ICMS)<br>Eindhoven Univeristy of Technology, TU/e<br>PO Box 513, HG -1.26<br>
5600 MB Eindhoven, The Netherlands<br>Tel +31 40 247 5349</span></font><span lang="EN"></span></p>
<p><font face="Arial" size="2"><span lang="EN" style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">"Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein</span></font><span lang="EN"></span></p>
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