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

[David]

On Tue, 2003-11-11 at 19:35, Yuhua Song wrote:
> 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)?

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. 
> 
> 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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