<div dir="ltr"><div>Hi,</div>
<div> </div>
<div>Can someone please provide me the link? I couldnt find the link in gromacs webpage related to these.also in wiki, this is not clearly described.<br><br></div>
<div class="gmail_quote">On Fri, Sep 5, 2008 at 2:47 AM, Xavier Periole <span dir="ltr"><<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d">On Thu, 4 Sep 2008 23:22:35 -0500<br> "NAMD GROMACS" <<a href="mailto:namd.gromacs@gmail.com" target="_blank">namd.gromacs@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br><br>I have a couple of questions regarding top file and forcefield.<br><br>1st, in the top file<br>
<br>[ angles ]<br>; ai aj ak funct c0 c1 c2<br>c3<br> 2 1 3 2 ga_9<br> 2 1 4 2 ga_9<br> 2 1 5 2 ga_10<br> 3 1 4 2 ga_9<br>
3 1 5 2 ga_10<br>Can you please tell me what the word "funct: stands for? what kind of<br>functionals, why the numbers 2, and then in case of angles it changes to 1?<br>I couldnt find good explanation for this in any manual or tutorial.<br>
</blockquote></div>there is chapter dedicted to this ... and there the wiki (link at <a href="http://www.gromacs.org/" target="_blank">www.gromacs.org</a>) ...
<div class="Ih2E3d"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Also what does ga_9, ga_10 etc means..I guess the a in ga stands for angle,<br>I dont know where the g is coming from. I am guessing the numbers are<br>
different types of bond.<br></blockquote></div>you should have a look at the paper of the force field.
<div class="Ih2E3d"><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Question regarding the force-field.<br><br>Select the Force Field:<br>0: GROMOS96 43a1 force field<br>
1: GROMOS96 43b1 vacuum force field<br>2: GROMOS96 43a2 force field (improved alkane dihedrals)<br>3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<br>5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<br>
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>7: [DEPRECATED] Gromacs force field (see manual)<br>8: [DEPRECATED] Gromacs force field with hydrogens for NMR<br>9: Encad all-atom force field, using scaled-down vacuum charges<br>
10: Encad all-atom force field, using full solvent charges<br><br>Here I am choosing 2 for my peptide in water run. I am wondering If I need<br>to study peptide-mineral surface interaction, what number should I chose? Is<br>
there a way I can go beyond 10, or can I dvelop my own force field, .top<br>file for interacting with mineral surface? Any suggestions on how to develop<br>new .top file including metals and metal oxide surfaces would be also great<br>
help.<br><br>Thanks<br><br>Subhashis<br></blockquote><br></div>-----------------------------------------------------<br>XAvier Periole - PhD<br><br>Molecular Dynamics Group / NMR and Computation<br>University of Groningen<br>
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