[gmx-users] NVE of water

[Andrea]

Thank you for your hints. I'll give it a try right now.

Regards,
Andrea

2010/3/1 Berk Hess <gmx3 at hotmail.com>

> Hi,
>
> Shake is not relevant for water and also a time step of 2 fs should be
> fine.
> The cut-off's are the problem. You have a buffer size of 0.1 nm,
> which is already smaller than 2 times the distance from the center of
> geometry
> of a water molecule to a hydrogen. You need some additional distance
> for water diffusion. I would use a buffer of 0.25 to 0.3 nm.
> You don't list you coulombtype setting. Use pme (or if you want perfect
> energy
> conservation: pme-switch), you can also use reaction-field-zero if you
> really don't
> want to use PME.
> Then use nstlist=-1, run a short simulation and check in at the end of your
> log file
> that the neighbor list lifetime is somewhere between 5 and 20 steps.
>
> We should have a wiki entry for such details. Maybe there is one, but I was
> too lazy
> to check or make one.
>
> Berk
>
> > Date: Mon, 1 Mar 2010 09:16:36 +0100
> > From: r.friedman at bioc.uzh.ch
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] NVE of water
>
> >
> > Hi Andrea,
> > Did you use double precision? Also, I'd try a lower dt (say 1fs) and
> > shake tolerance (maybe 1E-8).
> > Good luck,
> > Ran
> >
> > Andrea wrote:
> > > Dear users,
> > >
> > > for test purposes in order to set up a bigger system, I try to run NVE
> > > simulations of SPC water, but the energy increases very rapidely. My
> > > guess is that the cutoffs I use are not good for water. I that the
> > > case ( I would be grateful for a good reference for suitable SPC water
> > > parameters) or do I miss something else?
> > > My parameter file for the NVE is:
> > >
> > > title = NVE
> > > cpp = /lib/cpp
> > > integrator = md
> > > dt = 0.002 ; ps ! = 2 fs
> > > nsteps = 50000 ; total 100 ps
> > > nstxout = 5000
> > > nstvout = 5000
> > > nstxtcout = 0
> > > nstlog = 5000
> > > nstenergy = 5000
> > > nstlist = 10
> > > ns_type = grid
> > > rlist = 1.1
> > >
> > > unconstrained-start = yes
> > > constraints = all-bonds
> > > constraint_algorithm = shake
> > > shake_tol = 0.0001
> > > ;VdW
> > > vdwtype = Switch
> > > rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist
> > > rvdw_switch = 0.9
> > > gen_vel = no ; yes
> > > gen_temp = 300
> > > gen_seed = -1
> > > ;Temperature coupling
> > > tc_grps = system
> > > tcoupl = no ;nose-hoover
> > > tau_t = 0.1
> > > ref_t = 300
> > > ;Pressure coupling
> > > pcoupl = no
> > > optimize_fft = yes
> > >
> > > Any suggesions are really welcome.
> > >
> > > Thank you.
> > >
> > > Regards,
> > > Andrea Muntean
> >
> >
> > --
> > ------------------------------------------------------
> > Ran Friedman
> > Postdoctoral Fellow
> > Computational Structural Biology Group (A. Caflisch)
> > Department of Biochemistry
> > University of Zurich
> > Winterthurerstrasse 190
> > CH-8057 Zurich, Switzerland
> > Tel. +41-44-6355559
> > Email: r.friedman at bioc.uzh.ch
> > Skype: ran.friedman
> > ------------------------------------------------------
> >
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