[gmx-users] The Cut-off for coulombtype heat up the water system?

[Justin A. Lemkul]

Yanmei Song wrote:
> Dear Users:
> 
> I was running a system by non-equilibrium MD using a plain Cut-off for 
> the electrostatics:
> 
> title               =  water
> cpp                 =  /lib/cpp
> constraints         =  all_bonds
> integrator          =  md
> dt                  =  0.004   ; ps !
> nsteps              =  500000  ; total 8ns.
> nstcomm             =  1
> nstxout             =  50000
> nstvout             =  50000
> nstfout             =  0
> nstlog              =  5000
> nstenergy           =  5000
> nstxtcout           =  25000
> nstlist             =  10
> ns_type             =  grid
> pbc                 =  xyz
> coulombtype         =  Cut-off
> rlist               =  0.8
> rcoulomb            =  0.9
> rvdw                =  0.8
> fourierspacing      =  0.12
> ewald_rtol          =  1e-5
> ;nemd
> cos_acceleration    =  0.005
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc_grps             =  SOL
> tau_t               =  0.1
> ref_t               =  300
> ; Energy monitoring
> energygrps          =  SOL
> ; Isotropic pressure coupling is now on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> ;pc-grps            =  SOL
> tau_p               =  1.0
> ref_p               =  1.0
> compressibility     =  4.5e-5
> 
> ; Generate velocites is off at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  100000
> 
> I can not figure out where I did wrong, the temperature of the system is 
> 303.54 after 5ns run ( the temperature turns to 303 in 500ps). Thanks 
> for the help in advance!

Why are you using cutoff for coulombtype?  It is the reason for the heating you 
are seeing:

http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html

-Justin

> -- 
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
> 
> 
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-- 
========================================

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

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