<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi,<div><span class="Apple-style-span" style="font-family: Verdana, sans-serif, monospace; font-size: 11px; line-height: 13px; white-space: pre; ">#ifndef FLEXIBLE means not #ifdef FLEXIBLE? That is to say #ifndef FLEXIBLE means if not define?</span></div><div><font class="Apple-style-span" face="Verdana, sans-serif, monospace" size="3"><span class="Apple-style-span" style="font-size: 11px; line-height: 13px; white-space: pre;">in GMX4.0.7</span></font></div><div><font class="Apple-style-span" face="Verdana, sans-serif, monospace" size="3"><span class="Apple-style-span" style="font-size: 11px; line-height: 13px; white-space: pre;"><div>define = -DFLEXIBLE[ moleculetype ]</div><div>; molname<span class="Apple-tab-span" style="white-space:pre">        </span>nrexcl</div><div>SOL<span class="Apple-tab-span" style="white-space:pre">        
        </span>2</div><div><br></div><div>[ atoms ]</div><div>; id<span class="Apple-tab-span" style="white-space:pre">        </span>at type<span class="Apple-tab-span" style="white-space:pre">        </span>res nr <span class="Apple-tab-span" style="white-space:pre">        </span>residu name<span class="Apple-tab-span" style="white-space:pre">        </span>at name<span class="Apple-tab-span" style="white-space:pre">                </span>cg nr<span class="Apple-tab-span" style="white-space:pre">        </span>charge</div><div>#ifdef _FF_OPLS</div><div>1 opls_111 1 SOL OW 1 -0.834</div><div>2 opls_112 1 SOL HW1 1 0.417</div><div>3 opls_112 1 SOL
HW2 1 0.417</div><div>#endif</div><div>#ifdef _FF_CHARMM</div><div>1 OT 1 SOL OW 1 -0.834</div><div>2 HT 1 SOL HW1 1 0.417</div><div>3 HT 1 SOL HW2 1 0.417</div><div>#endif</div><div>#ifdef _FF_GROMACS </div><div>1 OWT3 1 SOL OW
1 -0.834</div><div>2 HW 1 SOL HW1 1 0.417</div><div>3 HW 1 SOL HW2 1 0.417</div><div>#endif</div><div>#ifdef _FF_GROMOS96</div><div>1 OWT3 1 SOL OW 1 -0.834</div><div>2 HW 1 SOL HW1 1 0.417</div><div>3 HW
1 SOL HW2 1 0.417</div><div>#endif</div><div><br></div><div>#ifdef FLEXIBLE</div><div>[ bonds ]</div><div>; i<span class="Apple-tab-span" style="white-space:pre">        </span>j<span class="Apple-tab-span" style="white-space:pre">        </span>funct<span class="Apple-tab-span" style="white-space:pre">        </span>length<span class="Apple-tab-span" style="white-space:pre">        </span>force.c.</div><div>1<span class="Apple-tab-span" style="white-space:pre">        </span>2<span class="Apple-tab-span" style="white-space:pre">        </span>1<span class="Apple-tab-span" style="white-space:pre">        </span>0.09572<span class="Apple-tab-span" style="white-space:pre">        </span>502416.0 0.09572<span class="Apple-tab-span" style="white-space:pre">        </span>502416.0 </div><div>1<span class="Apple-tab-span" style="white-space:pre">        </span>3<span
class="Apple-tab-span" style="white-space:pre">        </span>1<span class="Apple-tab-span" style="white-space:pre">        </span>0.09572<span class="Apple-tab-span" style="white-space:pre">        </span>502416.0 0.09572<span class="Apple-tab-span" style="white-space:pre">        </span>502416.0 </div><div><span class="Apple-tab-span" style="white-space:pre">        </span></div><div><br></div><div>[ angles ]</div><div>; i<span class="Apple-tab-span" style="white-space:pre">        </span>j<span class="Apple-tab-span" style="white-space:pre">        </span>k<span class="Apple-tab-span" style="white-space:pre">        </span>funct<span class="Apple-tab-span" style="white-space:pre">        </span>angle<span class="Apple-tab-span" style="white-space:pre">        </span>force.c.</div><div>2<span class="Apple-tab-span" style="white-space:pre">        </span>1<span class="Apple-tab-span" style="white-space:pre">        </span>3<span class="Apple-tab-span" style="white-space:pre">        </span>1<span class="Apple-tab-span"
style="white-space:pre">        </span>104.52<span class="Apple-tab-span" style="white-space:pre">        </span>628.02<span class="Apple-tab-span" style="white-space:pre">        </span>104.52<span class="Apple-tab-span" style="white-space:pre">        </span>628.02<span class="Apple-tab-span" style="white-space:pre">        </span></div><div><br></div><div>#else</div><div>[ settles ]</div><div>; i<span class="Apple-tab-span" style="white-space:pre">        </span>j<span class="Apple-tab-span" style="white-space:pre">        </span>funct<span class="Apple-tab-span" style="white-space:pre">        </span>length</div><div>1<span class="Apple-tab-span" style="white-space:pre">        </span>1<span class="Apple-tab-span" style="white-space:pre">        </span>0.09572<span class="Apple-tab-span" style="white-space:pre">        </span>0.15139</div><div><br></div><div>[ exclusions ]</div><div>1<span class="Apple-tab-span" style="white-space:pre">        </span>2<span class="Apple-tab-span" style="white-space:pre">        </span>3</div><div>2<span
class="Apple-tab-span" style="white-space:pre">        </span>1<span class="Apple-tab-span" style="white-space:pre">        </span>3</div><div>3<span class="Apple-tab-span" style="white-space:pre">        </span>1<span class="Apple-tab-span" style="white-space:pre">        </span>2</div><div>#endif</div><div><br></div><div>BUT in GMX4.5.1</div><div>[ moleculetype ]
; molname        nrexcl
SOL                2
[ atoms ]
; id        at type        res nr         residu name        at name                cg nr        charge
1 OWT3 1 SOL OW 1 -0.834
2 HW 1 SOL HW1 1 0.417
3 HW 1 SOL HW2 1 0.417
#ifndef FLEXIBLE
[ settles ]
; i        j        funct        length
1        1        0.09572        0.15139
[ exclusions ]
1        2        3
2        1        3
3        1        2
#else
[ bonds ]
; i        j        funct        length        force.c.
1        2        1        0.09572        502416.0 0.09572        502416.0
1        3        1        0.09572        502416.0 0.09572        502416.0
        
[ angles ]
; i        j        k        funct        angle        force.c.
2        1        3        1        104.52        628.02        104.52        628.02        
#endif
</div><div><br></div><div>I think they are the same. If I want to use FLEXIBLE water, I should add define = -DFLEXIBLE in .mdp file as in GMX4.0.7.</div><div>Is it right? Thanks!</div><div>Zhongjin He</div></span></font></div></td></tr></table><br>