Thanks, David. I look into this file, and I know I need to set vdwtype = user in *.mdp file.<br>
But I still don't know how to set [ nonbond_parms ] in force field file,<br>
which relate this table.xvg with two atoms type.<br>
This is my force field file. Could you tell me how to modify it to specify CH3 CH3 interaction as vdw potential in table.xvg<br>
<br>
-----------------------------------------------------------------------<br>
[ defaults ]<br>
1 1<br>
[ atomtypes ]<br>
;name mass charge
ptype
c6 c12<br>
;<br>
CH3 14.0000 0.000 A 2.36400e-03 1.59000e-06<br>
<br>
<br>
[ nonbond_params ]<br>
; i j func
c6 c12<br>
CH3 CH3 1 2.36400e-03 1.59000e-06<br>
----------------------------------------------------------------------------------------------<br><br><div><span class="gmail_quote">On 12/1/05, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">kun jiao wrote:<br><br>> Dear, Gromacs Community,
<br>> I am a new user of Gromacs. In my project I need to implement a<br>> very complicate vdw potential. I read the gromacs manual which said I<br>> need to prepare a table.xvg file.<br>> But I have no idea how this file looks like, and how to relate it with
<br>> top file ( how to specify nonbond_params ). Could anyone give me an<br>> example, such as table.xvg, *.top, *.itp ?.<br><br><br>in share/top you will find 6-12 etc. tables.<br>Basically you need<br>x fc(x) fc"(x) fd(x) fd"(x) fr(x) fr"(x)
<br>fc(x) will be multiplied by charges<br>fd(x) by dispersion constant (C6)<br>fr(x) by repulsion constant (C12)<br><br>> Any suggestion is appreciate:)<br>><br>> Regards,<br>> Kun<br>><br>>------------------------------------------------------------------------
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