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

[Yanmei Song]

Dear Justin:

Thank you so much for your answer. That helps a lot!

On Thu, Jun 18, 2009 at 10:35 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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?
>>
>>
> That is one of the known problems with using cut-off, yes.
>
> -Justin
>
>  On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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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>>
>>    --    ========================================
>>
>>    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
>>
>
> --
> ========================================
>
> 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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