[gmx-users] NVE of water

[Justin A. Lemkul]

Berk Hess wrote:
> 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.

There was a basic NVE page; I have updated it based on your notes above:

http://www.gromacs.org/Documentation/Terminology/NVE

-Justin

> 
> 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================