[gmx-users] Problems for Equilibration with 256 DPPC obtained from 64 DPPC

[Yuhua Song]

Thanks Anton.

> > 3) After I do the minimization of 256 DPPC, does that mean the
temperature
> > is 0K, I have to warm the system up to 300K before the production run?
>
> No, during minimization there is no velocity on the atoms, hence no
kinetic
> energy, hence no temperature. There are two ways to get the right system
> temperature: generate velocities from a maxwell distribution at the
> temperature you want (there is an option in the .mdp for that, and this
> is the way most people do it), or heat your system from 0K to the
temperature
> using simulated annealing (tricky, I don't normally do that).

after I equilibrate 64DPPC, then use genconf to duplicate to get 256DPPC, to
run NPT equilibration at 300K. Should I use velocity generation in the mdp
file? becuase available *.trj file that has the velocity informaiton is for
DPPC64, so I think that it may not be proper to read the read the velocity
info for DPPC256 from DPPC64 file, am I right? Also, in the tutoral on the
gromacs website about septitde case, for NVT, it use velocity generator, but
for NPT it did not use velocity generator and did not read the velocity from
the previous NVT step, does this mean that NPT production run, we did not
need to consider the velocity ( read in velocity or generate the velocity)?

Thanks,

Yuhua