Hi All,<br>I am trying to run simulated annealing for my protein + NDP kept in a water box.<br>I want to vary the temperature for the NDP only and want to keep the constant temperature for rest of the system.<br>for the same when tried with making two groups, one for NDP and other for rest of the molecule, and with the following params in .mdp<br>
....<br>energygrps = NDP excl_NDP<br>Tcoupl = berendsen<br>tau_t = 0.1 0.1<br>tc-grps = NDP excl_NDP<br>ref_t = 300 300<br>annealing = single single<br>
annealing_npoints = 5 0<br>annealing_time = 0 5 10 15 20<br>annealing_temp = 300 400 450 500 300<br>...<br>I am getting the following msg while doing grompp<br>_______________________<br>.<br>.<br>.<br>.<br>.<br>Simulated annealing for group NDP: Single, 5 timepoints<br>
Time (ps) Temperature (K)<br> 0.0 300.0<br> 5.0 400.0<br> 10.0 450.0<br> 15.0 500.0<br> 20.0- 300.0<br>Simulated annealing for group excl_NDP: Single, 0 timepoints<br>Time (ps) Temperature (K)<br>
Segmentation fault<br><br><br>while trying the same with only single group i.e. taking whole system for the simulated annealing <br>with following params in .mdp<br>...<br>energygrps = system<br>Tcoupl = berendsen<br>
tau_t = 0.1<br>tc-grps = system<br>ref_t = 300<br>annealing = single<br>annealing_npoints = 5<br>annealing_time = 0 5 10 15 20<br>annealing_temp = 300 400 450 500 300<br>......<br>
This run was running perfect with single group...<br>Please correct me if i am following wrong way for mentioning params., or Is there anything else to be taken care of...<br><br>Looking for suggestion and solutions..<br>
<br>With thanks,<br>Vivek<br><br><br>