[gmx-users] The Cut-off for coulombtype heat up the water system?
ysong30 at asu.edu
Thu Jun 18 19:27:11 CEST 2009
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
>> 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
>> 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:
>> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
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Department of Chemical Engineering
Arizona State University
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