[gmx-users] The Cut-off for coulombtype heat up the water system?
chihying2008 at gmail.com
Fri Jun 19 05:07:58 CEST 2009
People conclude that the heating up is normal by using a plain cut-off.
So, how to fix the problem?
1. From Berk => use multiple groups.
=> how ???
=> I have been thinking that it is better to group the molecule
=> such as: protein , non-protein
2. change the coulombtype without the coulomb cut-off rcoulomb ?
=> such as PME, PPPM ?
=> what's the suggestion about this?
3. Normally, how do people fix this problem?
No, this problem is not due to the Berendsen thermostat.
The integrations errors in the electrostatics have much more effect
on the water than on the protein, because the water has higher charges
and is far more mobile. No thermostat can correct for these errors,
unless you use multiple groups.
In addition the Berendsen thermostat will move energy from fast to
slow motions. This effects becomes much stronger when the thermostat
has to do a lot of scaling due to the heat generated by cut-off's.
Inaccurate constraining will remove heat from the system, but this
effect is orders of magnitude smaller than the Coulomb cut-off heating.
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
>> gmx-users mailing list gmx-users at gromacs.org
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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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