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

[Yanmei Song]

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> wrote:

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