Hi, <br><br> In the manual:<br><br>" Consider a water molecule interacting with another atom. When we would apply the cutoff an on atom-atom basis we might include the atom-Oxygen interaction(with a charge of -0.82) without<br>
the compensating charge of the protons and so induce a large dipole moment over the system. Therefore we have to keep groups of atoms with total charge 0 together. These groups are called charge groups.<br><br>So, When I tried to define energy groups based on chain id (energy_grps = chA chB) , I always get an error.<br>
<br>I don't understand why GROMACS give an option to define energy groups based on chain id.<br><br>Fatal error:<br>atoms 4176 and 4182 in charge group 1767 are in different energy groups<br><br>PDB:<br>ATOM 4176 OG SER A 541 -13.599 44.346 39.228 1.00 0.00 S 1<br>
ATOM 4177 N ALA A 542 -12.827 48.211 42.079 1.00 0.00 A 1<br>ATOM 4178 CA ALA A 542 -12.788 48.960 43.342 1.00 0.00 A 1<br>ATOM 4179 C ALA A 542 -12.052 50.279 43.097 1.00 0.00 A 1<br>
ATOM 4180 O ALA A 542 -12.096 50.830 41.993 1.00 0.00 A 1<br>ATOM 4181 CB ALA A 542 -12.084 48.160 44.447 1.00 0.00 A 1<br>ATOM 1 N THR B 1 22.984 77.078 8.100 1.00 20.55 T N<br>
<br><br clear="all"><br>-- <br>Shiyong Liu<br>Postdoc<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone:         (785) 864-1962<br>