Dear Gmx Users,<br><br>My system consists of a Tube made of Oxygen, Hydrogen and ions. These atoms are not connected via bonds. I try tu run EM:<br><br>; minim.mdp - used as input into grompp to generate em.tpr<br>; Parameters describing what to do, when to stop and what to save<br>
<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>emstep = 0.001 <br>nsteps = 50000 ; Maximum number of (minimization) steps to perform<br>
nstxout = 1<br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)<br>coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.4 ; Short-range electrostatic cut-off<br>
rvdw = 1.4 ; Short-range Van der Waals cut-off<br>pbc = xyz ; Periodic Boundary Conditions (yes/no)<br><br>freezegrps = TUB<br>freezedim = Y Y Y<br><br><br>Then a lot of errors "water molecule on atom X cannot be settled". I tried:<br>
<br>1. constraints = none<br><br>2. remove those water molecules - then other water molecules have the same error<br><br>3. using nstxout =1 in VMD, I could observe that some of the molecules facing this error split in one frame (hydrogens 7A away from oxygen) or spin around 180 degrees - it depends.<br>
<br>4. I tried increase vdwradii of the atoms which form my Tube so they wont overlap with water<br><br><br>If you have any suggestions I will really appreciate,<br><br>Steven<br><br><br><br>