On 2/03/2010 12:39 AM, Ran Friedman wrote:
Hi,
I would still argue that double precision is important.
Oh? The discussion of Table 4 of
http://pubs.acs.org/doi/abs/10.1021/ct700301q (2008 GROMACS 4 JCTC
paper) suggested to me that single-precision NVE could be done well in
GROMACS. Am I missing something?
Mark
My comment on SHAKE was based on CHARMM - in Gromacs it indeed doesn't
matter for water.
Ran
Justin A. Lemkul wrote:
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: [email protected]
> To: [email protected]
> 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: [email protected]
> Skype: ran.friedman
> ------------------------------------------------------
>
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