Dear Dr. Mark, <br><br>Thanks very much for pointing out that GROMACS can handle multiple instances of the parameters with different n for a single dihedral. <br><br>However, given that, in the existing ffamber ports in GROMACS the other dihedral parameters have been converted to RB form, would it make a difference to just import these new parameters in the non-RB form? <br>
<br>To my knowledge, the torsional term should not vary (or, vary within acceptable limits) irrespective of the functional form used to calculate it. But I would like to know if there could be some reason for which this assumption cannot be made. <br>
<br>Dear Dr. Alan, <br><br>Thanks very much for pointing out to the acpypi code. I was able to better understand the conversion procedure. <br><br>Sincerely, <br>Vignesh<br><br><div class="gmail_quote">On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Users,<br>
<br>
I am trying to port the new parmbsc0 forcefield<br>
(<a href="http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0" target="_blank">http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0</a>) into gromacs for DNA<br>
simulations.<br>
<br>
While unit conversions are sufficient to convert many of the parameters<br>
from AMBER to GROMACS format, dihedral angle conversion does not seem to<br>
be straight forward - the dihedral parameters need to be converted to<br>
the Ryckaert-Bellemans parameters.<br>
</blockquote>
<br></div>
Why? GROMACS can probably do the non-RB form - IIRC you can implement a sum of multiple instances of 4.61 with different n.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I went through the GROMACS 4.0<br>
manual, especially equations 4.61-4.65 to understand the procedure. The<br>
procedure involves comparing the fourier expansion of the IUPAC<br>
convention of dihedral potential (equation 4.65) with the<br>
Ryckaert-Bellemans (RB) functional of dihedral potential (equation 4.62)<br>
to get the Cn's of the RB function. However, I am not able to understand<br>
how to account for the phase angles. (Also to note, the parmbsc0<br>
forcefield contains phase angles other than 0 and 180.)<br>
</blockquote>
<br></div>
Elegant conversion formulae require those angles to be convenient...<br>
<br>
Mark<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Any advice or suggestion will be of great help.<br>
<br>
Thank you,<br>
<br>
Vignesh<br>
<br>
--<br>
R.Vigneshwar<br>
Graduate Student,<br>
Dept. of Chemical & Biomolecular Engg,<br>
National University of Singapore,<br>
Singapore<br>
<br>
"Strive for Excellence, Never be satisfied with the second Best!!"<br>
<br>
I arise in the morning torn between a desire to improve the world and a<br>
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)<br>
<br>
</blockquote></div></div><font color="#888888">
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</font></blockquote></div><br><br clear="all"><br>-- <br>R.Vigneshwar<br>Graduate Student,<br>Dept. of Chemical & Biomolecular Engg,<br>National University of Singapore,<br>Singapore<br><br>"Strive for Excellence, Never be satisfied with the second Best!!"<br>
<br>I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)<br>