Dear Martin<br><br>As Mark has already told you - if you have a problem with gromacs email the list and wait for a reply. Don't just email people you don't know from Adam and expect them to reply because "you are in a rush." The file that you have read from the mailing list contains everything I know about tabulated potentials in gromacs. I can't say I fully understand your email but I think that your questions (other than the stuff on bonded potentials) are all covered on the wikki page and certainly are covered in the pdf file I wrote. <br>
<br>In short<br><br>>For the bonding part I have the following table files:<br>
<br>
>table_b1.xvg<br>
>table_a1.xvg<br>
>table_a2.xvg<br>
>table_a3.xvg<br><br>I know nothing about using tabulated potentials for bonded interactions. If this is what is in the manual though its probably right.<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Must I write<br>
<br>
energygrps = A B C<br>
energygrp_table = AC BB BC<br>
<br>
in the mdp file and use the tables<br>
<br>
table.xvg This has the A B interaction in?<br>
table_A_C.xvg<br>
table_B_B.xvg<br>
table_B_C.xvg<br>
<br>
with the command line for mdrun saying -table table.xvg?<br></blockquote><div><br>Yes this is exactly what the wikki tells you to do. Why do you think it wont work in your case? Incidentally, you can work out if this is working by doing one md step in gromacs and comparing the energy you obtain with the energy you get from another code, which you are confident produces correct energies. <br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Another thing, because the tables doesn't have to contain only zero columns...<br>
Can I put anything on the f and f' columns (because the charge of my<br>
atoms is zero)?<br></blockquote><div><br>Yes. I always use f=1/r even though I know it will be ignored (with this choice f'=1/r**2 obviously)<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Can I put (for example) 0.5 in the g and g' columns and my potential<br>
(and the force) minus 0.5 in columns h and h'?<br></blockquote><div><br>I don't understand what you want to do here. If you put 0.5 in g then g'=0, which you can work out using, what I assume, is the first thing you learnt about calculus. <br>
</div></div><br>ciao<br>Gareth<br><br>