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On 16/02/2011 3:41 PM, Mr Bernard Ramos wrote:
<blockquote cite="mid:151297.44127.qm@web52701.mail.re2.yahoo.com"
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<div><span style="font-size: 10pt; font-family: Arial;">Hi
everyone!<o:p></o:p></span></div>
<div><span style="font-size: 10pt; font-family: Arial;"> <o:p></o:p></span></div>
<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). <o:p></o:p></span></div>
<div><span style="font-size: 10pt; font-family: Arial;"> <o:p></o:p></span></div>
<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>
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<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>
<blockquote cite="mid:151297.44127.qm@web52701.mail.re2.yahoo.com"
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<div><span style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></div>
<div><span style="font-size: 10pt; font-family: Arial;"> <o:p></o:p></span></div>
<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>
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<br>
Preferably as a sum of existing functional forms. Or use tabulated
bonded interactions (see manual and wiki).<br>
<br>
Mark<br>
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