Hi all,<br><br>I found that the 99SB force field in AMBERTOOLS1.5 and GROMACS4.5.4 have different force constants for bond and angle parameters, after converting them to the same unit.<br><br>So for those in AMBER<br>[ moleculetype ]<br>
; molname nrexcl ; <span class="il">TIP3P</span> model<br> WAT 2<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass<br>
1 OW 1 WAT O 1 -0.834 16.00000<br> 2 HW 1 WAT H1 1 0.417 1.00800<br> 3 HW 1 WAT H2 1 0.417 1.00800<br><br>#ifdef FLEXIBLE<br>
[ bonds ]<br>; i j funct length force.c.<br>1 2 1 0.09572 462750.4 0.09572 462750.4<br>1 3 1 0.09572 462750.4 0.09572 462750.4<br><br>[ angles ]<br>; i j k funct angle force.c.<br>2 1 3 1 104.520 836.800 104.520 836.800<br>
#else<br>[ settles ]<br>; i j funct length<br>1 1 0.09572 0.15139<br><br>[ exclusions ]<br>1 2 3<br>2 1 3<br>3 1 2<br>#endif<br><br><br><br><br><br><br>while for GROMACS, that is, in the amber99sb.ff/<span class="il">tip3p</span>.itp file,<br>
<br>[ moleculetype ]<br>
; molname nrexcl<br>SOL 2<br><br>[ atoms ]<br>; id at type res nr res name at name cg nr charge mass<br> 1 OW 1 SOL OW 1 -0.834 16.00000<br> 2 HW 1 SOL HW1 1 0.417 1.00800<br>
3 HW 1 SOL HW2 1 0.417 1.00800<br><br>#ifndef FLEXIBLE<br><br>[ settles ]<br>; OW funct doh dhh<br>1 1 0.09572 0.15139<br><br>[ exclusions ]<br>1 2 3<br>
2 1 3<br>3 1 2<br><br>#else<br><br>[ bonds ]<br>; i j funct length force_constant<br>1 2 1 0.09572 502416.0 0.09572 502416.0<br>1 3 1 0.09572 502416.0 0.09572 502416.0<br>
<br><br>[ angles ]<br>; i j k funct angle force_constant<br>2 1 3 1 104.52 628.02 104.52 628.02<br><br>#endif<br><br><br><br>So I wonder why different parameters for tip3p water are used in GMX, even for the save force field ?<br>
<br>Thanks for any suggestion,<br><br>Yun<br>