<p>Hi Lina,</p>
<p>Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump</p>
<p>Hope it helps,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Oct 28, 2011 6:27 AM, "lina" <<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>> wrote:<br><br><p><font color="#500050">On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:
> Hi Lina,
>
> Make su...</font></p>I used the initial mdrun .tpr. After checking the generated pdb (total<br>
51 frames), the first 28/29 frames both are together, but later are<br>
separated. (the intra_fit also not work as expected).<br>
<br>
So I think at beginning the reference initial ones are together.<br>
<br>
This .xtc were trjcat together, first 200ns and then extend to 500ns,<br>
the .pdb generated used dt 10ns.<br>
><br>
> Cheers,<br>
Am I wrong in some places? Actually for other trajectories I had no<br>
problem (use the same way of handling it).<br>
<br>
Thanks,<br>
<p><font color="#500050">>
> Tsjerk
>
> On Oct 27, 2011 11:47 AM, "lina" <<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>> wrote:
>
> Hi,
>
> I have ...</font></p></blockquote></p>