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<div style="">Dear all,<br>
<br>
I am setting-up a simulation of a protein-DNA complex using amber force field.<br>
<br>
In the manual (v4.5.3) I have found the recommended cutoff distances for electrostatics - coulombtype using PME (rcoulomb=rlist=rvdw = 0.9nm) with Gromos ff. However, I am aware the cutoff values are specific for different forcefield and also the simulated
system. <br>
<br>
Since I am using the amber ff with Gromacs, I wanted to ensure I set-up the correct cutoffs to prevent any potential artifacts, so I have searched the manual, gmx-users old posts (gromacs wiki links do not work any more) and papers, and I found all sorts of
distances for the non-bonded interactions tratment with PME (ranging from 1.0 to 1.4 nm).
<br>
With respect to the amber ff, I found a value of 0.8nm cutoff for the PME in the Amber manual.
<br>
<br>
Could you please advise me on what would be the reasonable cutoff values to choose for the protein-DNA system, with the use of Gromacs 4.5.3 and amber ff?
<br>
All your comments will be greatly appreciated.<br>
<br>
Thank you<br>
Jarmila<br>
<br>
<br>
<br>
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<div style="font-family: Tahoma; font-size: 13px;"><font class="Apple-style-span" color="#000080">Jarmila Husby, </font><span class="Apple-style-span" style="color: rgb(0, 0, 128);">PhD Candidate</span></div>
<div style="font-family: Tahoma; font-size: 13px;">
<div><font class="Apple-style-span" color="#000080">CRUK PPI Drug Discovery/ BMSG Group</font></div>
<div><font class="Apple-style-span" color="#000080">Department of Pharm & Biol Chemistry</font></div>
<div><font class="Apple-style-span" color="#000080">The School of Pharmacy, University of London</font></div>
<div><font class="Apple-style-span" color="#000080">email: jarmila.husby@live.pharmacy.ac.uk</font></div>
<div><span class="Apple-style-span" style="font-family: Arial,sans-serif;"><font class="Apple-style-span" color="#000080">tel: (44) 0207 753 5996</font></span></div>
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