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

[David]

On Tue, 2003-11-11 at 22:50, Yuhua Song wrote:
> 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?
yes, check any confout.gro you will find six columns
> 
> 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.
> 
his works fine and gives you binary precision for your velocities and
coordinates. However, since your changing the simulation  protocol  your
trajectory is discontinuous anyway, so here it is not that important.
When using continuation simulations it is however (use tpbconv for
that!)

> Thanks
> 
> Yuhua
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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