<span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(34,34,34)">Hi Catherine,<br>you should install any <span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">gromacs</span> <b>4.5.x</b>, and then you can use <span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">gromacs</span><br>
with each trajectory supported by <span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">VMD</span> because <span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">gromacs</span> is able to use <span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">VMD</span> plugin to<br>
perform trajectory reading.<br>Basically:<br>1) Install the latest <span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">gromacs</span> version<br>
2) Install <span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">VMD</span><br>3) Set the variable VMD_PLUGIN_PATH to contain the complete path of the molfile <span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">vmd</span> directory.<br>
In my case, for example: VMD_PLUGIN_PATH=/apps/<span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">vmd</span>/1.9/<u></u>lib/<span style="background-image:initial;background-color:rgb(255,255,204);color:rgb(34,34,34);background-repeat:initial initial">vmd</span>/plugins/LINUXAMD64/<u></u>molfile<br>
<br>Francesco<br></span><br><div class="gmail_quote">Il giorno 08 marzo 2012 17:40, a a <span dir="ltr"><<a href="mailto:patd_2@hotmail.com" target="_blank">patd_2@hotmail.com</a>></span> ha scritto:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div dir="ltr">
Dear Sir/Madam,<div><br></div><div>I learnt that we can use mdcrd from AMBER directly.</div><div><br></div><div>I have used the following commands.</div><div><br></div><div>/share1/gromacs/bin/g_covar -s xxx.pdb -f xxx.mdcrd -o -v</div>
<div><br></div><div>An error message was obtained.</div><div><br></div><div><div>Program g_covar, VERSION 4.0.7</div><div>Source code file: gmxfio.c, line: 737</div><div><br></div><div>Can not open file:</div><div>md0.mdcrd.xtc</div>
</div><div><br></div><div>Did I do anything wrong?</div><div><br></div><div>Best regards,</div><div><br></div><div>Catherine</div><div><br></div><div><br></div> </div></div>
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