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

[David van der Spoel]

Yanmei Song wrote:
> Dear Justin:
> 
> Thanks for your response.
> 
> The reason I am doing this is that I wanted to test what the different 
> electrostatics treatments will affect my results. So the heating up is 
> normal by using a plain cut-off and the results can not be trusted, right?
> 
> On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
That is correct. Check J. Chem. Theor. Comp. 2 (2006) p. 1-11.

> 
> 
>     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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> 
> 
> -- 
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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