<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Thanks for the reply on my first querry. I have another one. If I add a NEW atom type in *.atp file, will Gromacs automatically recognize this atom type? </DIV>
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<DIV>Thanks. </DIV>
<DIV><BR><BR>--- On <B>Wed, 2/16/11, Mark Abraham <I><Mark.Abraham@anu.edu.au></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Mark Abraham <Mark.Abraham@anu.edu.au><BR>Subject: Re: [gmx-users] on force fields<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Wednesday, February 16, 2011, 1:53 PM<BR><BR>
<DIV id=yiv1010603858>On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote:
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<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hi everyone!</SPAN></DIV>
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<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">I need to update the gromos force field 53A6 with the new force field 53ACARBO (JCC 10 NOV 2010). </SPAN></DIV>
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<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">1. I will have to change the parameter values in the file ff_bonded.itp and ff_nonbonded.itp in the gromos53a6.ff. Are these the only files that I need to update if I need to switch to a new force field?</SPAN></DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE><BR>You should make a copy of the whole force field directory into your working directory, rename the new directory suitably, make a suitable change to forcefield.doc, and then edit .itp files suitably. This means you're leaving your reference version untouched and can edit locally to your heart's content, and can be sure you're selecting the right force field with pdb2gmx and/or in your .top file.<BR><BR>
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<DIV><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">2. The new force field 53ACARBO has a new gromos functional form for select torsional potentials. How to I go over implementing this in gromos?</SPAN></DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE><BR>Preferably as a sum of existing functional forms. Or use tabulated bonded interactions (see manual and wiki).<BR><BR>Mark<BR></DIV><BR>-----Inline Attachment Follows-----<BR><BR>
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