Dear Gmx Users, I am running TPI of the water in the system containing free amino acids. Steps:
1. I run the NPT simulation of 100 ns to equilibrate the system. 2. I added 1 extra water molecule to the final pdb file (converted from gro) and to topology 3. I creaded tpi.tpr using grompp using new pdb file with extra water molecule 4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg -tpid tpid298.xvg My question: Is it better generate new velocities in my mdp file (continuation = yes, gen_vel = no, tpi integrator) for a pdb file or use velocities from previous simulations (gro file)? If the second option is more appropriate what velocity shall I adjust to the extra water molecule? I will appreciate your reply. Steven
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