Thanks Ilja,<br><br><div class="gmail_quote">On Tue, Jul 27, 2010 at 16:36, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div id=":2rj" class="ii gt">I think the bond terms differ simply due to the round off error. The gro<br>
file is worse than pdb when it comes to round off in Cartesian coordinates.<br>
You can confirm this is the case by taking your gro file and converting it<br>
back to pdb using gromacs tools and then use the resulting pdb (with the<br>
same round of as the gro file now) file from gromacs in NAMD. You should see<br>
the same numbers for bonded terms then.<br></div></blockquote></div><br>I doubt that would do any difference.<div><br></div><div>Anyway, I tested with double precision and found out that my gro file is still rounded off like in single precision, i.e., my gro in double is the same in single and I was not expecting that.<div>
<br></div><div>Example:</div><div><br></div><div>pdb: 13 N ALA A 2 1.927 1.789 1.165 1.00 0.00</div><div><br></div><div>gro (single or double): 2ALA N 13 0.193 0.179 0.117<br clear="all"><br>
</div><div><br></div><div>I was expecting gro when using pdb2gmx_d to be like:</div><div><br></div><div>gro (single or double): 2ALA N 13 0.192700 0.178900 0.165000</div><div><br></div><div>Hummm.... I don't like this.</div>
<div><br></div><div><br></div><div>Alan<br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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