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

[Yuhua Song]

Thanks David.
> > 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)?
>
> Actually the velocities are in the gro file (in the speptide case). You
> can use velocity generation for your big system, it might equilibrate a
> bit faster.
> >
In my understanding, *.gro file is conformation file, it only has the
coordinate information, does it also has velocity information?

if I run a system first NVT, then NPt, my understanding is that I use
"grompp" to be able to read in the velocity from *.trj generated from NVT,
then use it to NPT, am I right? if not, please correct me.

Thanks

Yuhua