<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Mark<br><br>Many thanks<br><br>Chrysostomos<br><br>--- Στις <b>Πέμ., 08/07/10, ο/η Mark Abraham <i><mark.abraham@anu.edu.au></i></b> έγραψε:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>Από: Mark Abraham <mark.abraham@anu.edu.au><br>Θέμα: Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96<br>Προς: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Ημερομηνία: Πέμπτη, 8 Ιούλιος 2010, 4:49<br><br><div id="yiv456437303"><br><br>----- Original Message -----<br>From: "C. Batistakis" <cbatiss@yahoo.gr><br>Date: Wednesday, July 7, 2010 23:19<br>Subject: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96<br>To: gromacs <gmx-users@gromacs.org><br><br><table border="0" cellpadding="0"
cellspacing="0"><tbody><tr><td style="font: inherit;" valign="top"><style><!--#yiv456437303 _filtered #yiv456437303 {font-family:"Cambria Math";panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv456437303 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}#yiv456437303 #yiv456437303 p.MsoNormal, #yiv456437303 li.MsoNormal, #yiv456437303 div.MsoNormal {margin-top:0in;margin-right:0in;margin-bottom:10.0pt;margin-left:0in;line-height:115%;font-size:11.0pt;font-family:"sans-serif";}#yiv456437303 .MsoChpDefault {}#yiv456437303 .MsoPapDefault {margin-bottom:10.0pt;line-height:115%;} _filtered #yiv456437303 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv456437303 div.WordSection1 {}--></style> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Dear all</span></p> <p class="MsoNormal"
style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;"> </span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">> I am trying to simulate Nitrile-Butadiene-Rubber, using the Gromos96 force field. <br></span></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><br></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;">Let the availability of suitable parameters choose the force field :-)<br></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><br><span style="font-size: 12pt;"></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">> I have difficulties in finding the correct parameters from the bon.itp file , in order to define the polymer in the .rtp file.</span></p><p class="MsoNormal" style="margin-bottom:
0.0001pt; line-height: normal;"><br></p><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;">A first port of call would have been the appropriate paper for the force field - which might have made clear whether or not nitrile parameters were likely to be found.<br><span style="font-size: 12pt;"></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;"> </span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">> Can someone suggest which parameters I shall choose in the following:</span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><b><span style="font-size: 12pt;">In Bond-stretching parameters</span></b><span style="font-size: 12pt;"></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><b><span style="font-size:
12pt;"> For:</span></b><span style="font-size: 12pt;"></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">1) Triple bond between Carbon and Nitrogen (gb_????)</span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">2) Double bond CH=CH (gb_????)</span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;"> </span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><b><span style="font-size: 12pt;">In Bond-angle bending parameters </span></b><span style="font-size: 12pt;"></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><b><span style="font-size: 12pt;">
For:</span></b><span style="font-size: 12pt;"></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">1) CH<sub>2</sub>-CH=CH (ga_????)</span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">2) CH-C≡N (ga_????)</span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;"> </span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><b><span style="font-size: 12pt;">In Dihedral-angle type code</span></b><span style="font-size: 12pt;"></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><b><span style="font-size: 12pt;"> For:</span></b><span style="font-size:
12pt;"></span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">1) CH<sub>2</sub>-CH=CH-CH<sub>2 </sub>(gd_????)</span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">2) CH<sub>2</sub>-CH-C≡N (gd_????)</span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;"> </span></p> <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 12pt;">> If these parameters do not exist in this force field, can you suggest me another one to use?</span></p></td></tr></tbody></table><br>As a first step, try "grep nitrile *.atp" to see which of the atom type databases have nitrile in them. AMBER
forcefields are probably also OK, but you'll have to install them seperately.<br><br>Mark
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