[gmx-users] NVE of water

[Berk Hess]

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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