You are right, Mark. Thank you very much for your suggestions.<br><br>Jicun<br><br><div class="gmail_quote">2012/10/1 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">On 2/10/2012 8:22 AM, Jicun Li wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Maybe the fixed-format gro file is easier to code with in native F77, but it's difficult to prepare with other molecule building software.<br>
</blockquote>
<br></div>
Sure, but once you've picked a file format, you're stuck with it for a long time.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I would like Gromacs to read in the structure exactly, at least as exact as g96 file. But I do not like to use g96 file because there is no atom name in it. I can not use other software to view the structure.<br>
</blockquote>
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There's a separate library of code available on the website for linking to external projects that want to write GROMACS-readable trajectory file formats. That might be useful for you.<br>
<br>
Wanting to write the atom names in the trajectory file is wasteful if you have a big trajectory. For this reason, tools like GROMACS and VMD can read a structure file and then import a trajectory file that lacks atom information but whose atom ordering matches.<br>
<br>
You'll be much better off using tools that suit the job at hand:<br>
* When you want to view the structure, write a structure file because it has atom names and stuff.<br>
* When you want a high-precision trajectory, write a trajectory file because it has high precision.<br>
* When you want to view a trajectory, import the latter onto the former. You may wish to reconsider your choice of viewer if you can't do this :-)<div class="HOEnZb"><div class="h5"><br>
<br>
Mark<br>
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