<html>
<br>
<head>
<meta content="text/html; charset=iso-8859-1" http-equiv="Content-Type">
</head>
<body>
<font face="Times New Roman" size=3>
Dear Anton,
</font><br>
<font face="Times New Roman" size=3>
>> I want to use the RB potential for simulation
</font><br>
<font face="Times New Roman" size=3>
>> of a amorphous PE box containing 20 chains.
</font><br>
<font face="Times New Roman" size=3>
>> To this I changed the dihedral type to "3".
</font><br>
<font face="Times New Roman" size=3>
>> How can I make sure that the 1,4 interactions
</font><br>
<font face="Times New Roman" size=3>
>> are removed?
</font><br>
<font face="Times New Roman" size=3>
>> If I used pdb2gmx to generate the topology file
</font><br>
<font face="Times New Roman" size=3>
>> I allways get a [pairs] section. Do I have
</font><br>
<font face="Times New Roman" size=3>
>> to delete this manually?
</font><br>
<br>
<font face="Times New Roman" size=3>
>You'll have to add a pair definition for each 1-4 interaction
</font><br>
<font face="Times New Roman" size=3>
>that you want removed. If you used pdb2gmx, they should already
</font><br>
<font face="Times New Roman" size=3>
>be there, so I don't see that you would need to add or remove
</font><br>
<font face="Times New Roman" size=3>
>anything manually. Simply changing dihedral type should work.
</font><br>
<font face="Times New Roman" size=3>
>--
</font><br>
<font face="Times New Roman" size=3>
>Groetjes,
</font><br>
<font face="Times New Roman" size=3>
>Anton
</font><br>
<br>
<font face="Times New Roman" size=3>
Indeed I have the pair definition in my topol_?.itp files.
</font><br>
<font face="Times New Roman" size=3>
But, if the 1,4 interactions are removed in this way,
</font><br>
<font face="Times New Roman" size=3>
why do I see a LJ-14 energy term in the md.log
</font><br>
<font face="Times New Roman" size=3>
file as well as the g_energy program. Shouldn't this
</font><br>
<font face="Times New Roman" size=3>
contribution be zero if I exclude the 1,4 interactions
</font><br>
<font face="Times New Roman" size=3>
with the RB potential?
</font><br>
<br>
<font face="Times New Roman" size=3>
And why do I need a [pairtypes] entry for my CH2
</font><br>
<font face="Times New Roman" size=3>
atom type in the ffgmxnb.itp file to run grompp successfully?
</font><br>
<font face="Times New Roman" size=3>
I guessed that this is not needed if 1,4 interactions are
</font><br>
<font face="Times New Roman" size=3>
excluded.
</font><br>
<br>
<font face="Times New Roman" size=3>
Thanks,
</font><br>
<font face="Times New Roman" size=3>
Gitta
</font><br>
<br>
<br>
</body>
</html>