Dear ALL<br> <br> when we simulate in vaccum, first we do steepest descent, then conj, then md in vac. <br> I want to know that, Do we use periodic boundary conditions here..and also if we dont specify anything about pbc in mdp file wht does gromacs take it as...<br> <br> Also please tell me, is their any particular value of emtol in mdp files of steep and cg, that we should use... I use emtol=1000 in the steep file, and then when i do cg i keep it 100, 50, 10, 8, 2 step by step.<br> <br> Regards<br> nur<br> <p> 
        
        
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