[gmx-users] NVE of water

[Berk Hess]

Hi,

I have now added a check to grompp for the charge-group radii versus the buffer size
for the next Gromacs release.

Berk

Date: Mon, 1 Mar 2010 09:33:13 +0100
Subject: Re: [gmx-users] NVE of water
From: andreamuntean at gmail.com
To: gmx-users at gromacs.org

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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