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hi all,<br>
i am just an intermediate guy with gromacs now.<br>
i tried to view the final xtc file in vmd.<br>
in the first protein, i was sucessful in viewing it.<br>
In my second protein, it says error in number of atoms.so i had to convert it in to a format with a xtc file having only the protein molecules,according to a "dynatraj" website.<br>
I did it with trjconv.It showed me a very bad output of only lines.<br>
So i redid the whole process and got another output.The same problem persists in vmd.<br>
The important thing being that the outputs were viewable in ngmx under all conditions.<br>
i don't know where the problem is, is it in vmd or some bug in trjconv.From the lines output, i think it has something to do with the data for bond formation not being present in it.Is my prediction correct?<br>
Another query,<br>
i have done so much of experimentation that i now don't know what will be ideal mdp file parameters for cytosolic proteins.Can someone send me those.<br>
Thanks in advance.<br>
cheers<br>
hayagreevan
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