[gmx-users] NVE of water

[Ran Friedman]

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


-- 
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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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