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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi all,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
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?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I’ll appreciate any pointers in this direction.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thanks!<o:p></o:p></span></font></p>
<p><font size=2 face=Arial><span lang=EN style='font-size:10.0pt;font-family:
Arial'>--<br>
Pablo Englebienne, PhD<br>
<st1:place w:st="on"><st1:PlaceType w:st="on">Institute</st1:PlaceType> of <st1:PlaceName
w:st="on">Complex</st1:PlaceName></st1:place> Molecular Systems (ICMS)<br>
<st1:place w:st="on"><st1:City w:st="on">Eindhoven</st1:City></st1:place>
Univeristy of Technology, TU/e<br>
<st1:address w:st="on"><st1:Street w:st="on">PO Box</st1:Street> 513</st1:address>,
HG -1.26<br>
5600 MB <st1:City w:st="on">Eindhoven</st1:City>, The <st1:place w:st="on"><st1:country-region
w:st="on">Netherlands</st1:country-region></st1:place><br>
Tel +31 40 247 5349</span></font><span lang=EN><o:p></o:p></span></p>
<p><font size=2 face=Arial><span lang=EN style='font-size:10.0pt;font-family:
Arial'>"Progress is made by lazy men looking for easier ways to do
things." - Robert A. Heinlein</span></font><span lang=EN><o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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