Hi Esteban and Vitaly,<br>Thanks for your respose, I tried "trjconv" with -pbc mol while generating movie and it worked this time. <br><br>regards,<br>vivek<br><br><div class="gmail_quote">On 12 July 2010 16:01, Vitaly Chaban <span dir="ltr"><<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hmm... Straight lines... Is it VMD that your used to visualize the trajectory?<br>
<br>
I think this is just due to PBC. Compute some RDFs and they will give<br>
you an answer if your system is healthy.<br>
<br>
Dr. Vitaly Chaban<br>
<div class="im"><br>
<br>
<br>
> I am trying to run MD simulation for octanol using GROMACS, I have<br>
> downloaded the octanol.tar.gz from the user contributed section<br>
> <a href="http://www.gromacs.org/@api/deki/files/18/=octanol.tar.gz" target="_blank">http://www.gromacs.org/@api/deki/files/18/=octanol.tar.gz</a>.<br>
> When I performed this MD run according to the run input file and molecule<br>
> topology provided in this download, I observed straight lines in the system<br>
> while visualizing the trajectory. Can anybody suggest if there is any<br>
> problems in the run parameters provided or it is some mistake at my part ?<br>
> As a first thought It seems like a boundary condition problem to me. Any<br>
> insight into this will be really helpful for me.<br>
> Is there any other source for getting required information for octanol.<br>
> My final target is to run MD in water/octanol box. Please guide me with dos<br>
> and donts, If anybody has attempted for the same.<br>
</div>--<br>
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