<table cellspacing='0' cellpadding='0' border='0' ><tr><td valign='top' style='font: inherit;'>Dear Sir or Madam,<br><br>For the version 3.3.2 the gromacs switch potential function is the following :<br><br> Elja1 = (4.d0*eps1*sig1**6) * &<br> -(1.d0/r(i)**6) * &<br> (1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 &<br>
+ 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 &<br> - 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5)<br> Elja2 = (4.d0*eps1*sig1**12) * &<br> (1.d0/r(i)**12) * &<br>
(1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 &<br> + 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 &<br> - 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5)<br><br>Switch = Elja1 + Elja2<br><br>Remarks:<br>i) This is tested only when in the mdp file the vdw-type = Switch<br>ii) The Elja1 is the dispersion part of the potential (not the force).<br>iii) The Elja2 it the repulsion part of the potential (not the force).<br>iv) eps is the value of epsilon and sig is the value of sigma<br>v) r1 = rvdw-switch and rc1 = rvdw<br>vii) The function of the manual that sais that it applies Phi(r) both on switch and shift option doesn't seem to apply
in the switch case.<br>vii) Someone can find out if someone searches at : a)/root/Desktop/software/gromacs/gromacs-3.3.2/src/mdlib/<br>b)The file is called tables.c<br>c)look under if (bSwitch), where it sais swi<br>d)for pow look at the beginning<br>e)for Vtab under the cases etabLJ6 and etabLJ12<br>f)for whole under if ((r_r1) && bSwitch) , that is the multiplication of the dispersion and repulsion part with swi<br>g)in order to have units of energy someone must to multiply the above with 4*epsilon*sigma**6 for the dispersion part and 4*epsilon*sigma**12 for the repulsion part<br><br>Yours Sincerely,<br>Nikos<br></td></tr></table><br>
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