In selecting the eigen vector i just want to make sure about my consideration about the time frames. Should i need to consider the time frame t= 0.0 or i need to start at non zero positive numbers? Thank you.<br>Rama<br><br>
<div class="gmail_quote">On Fri, Oct 15, 2010 at 11:00 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</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;">
Hi Rama,<br>
<br>
You can convert the .trr file to readable .gro/.g96 with trjconv.<br>
Frames with positive times will correspond to eigenvectors; the time<br>
indicates the eigenvector index. Make sure not to use any options like<br>
pbc/fitting :p<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G <<a href="mailto:gtrama@gmail.com">gtrama@gmail.com</a>> wrote:<br>
> Hi,<br>
> Can anyone help to get the eigen vector in ascii format. I have with me the<br>
> trajectory file 'eigenvec.trr'.<br>
><br>
> On using g_covar_d, i got the the ascii format file 'covar.dat' and it has<br>
> covariance matrix of 3(NxN) number. But i am not interested in that.<br>
><br>
> I am interested in getting the ascii(readable) format of eigenvector and<br>
> hessian.mtx .<br>
> Your help is highly appreciated. Thank you.<br>
><br>
> with regards,<br>
> Rama<br>
><br>
> On Fri, Oct 15, 2010 at 2:29 PM, Ramachandran G <<a href="mailto:gtrama@gmail.com">gtrama@gmail.com</a>> wrote:<br>
>><br>
>> Hi gmx users:<br>
>> I did normal mode analysis and got the hessian.mtx . Using the command<br>
>> g_nmeig_d on the hessian.mtx<br>
>> i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr.<br>
>><br>
>> I need the complete eigenvector in the readable format. How i can get it?<br>
>> Thank you.<br>
>><br>
>> with regards,<br>
>> Rama<br>
>><br>
>> --<br>
>> Postdoctoral Research Scholar,<br>
>> Department of Chemistry,<br>
>> University of Nevada, Reno.<br>
><br>
><br>
><br>
><br>
><br>
</div></div>> --<br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<font color="#888888">--<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Postdoctoral Research Scholar,<br>Department of Chemistry,<br>University of Nevada, Reno.<br>