[gmx-users] Pressure coupling and cut-off
Justin A. Lemkul
jalemkul at vt.edu
Fri May 15 18:56:28 CEST 2009
Yanmei Song wrote:
> Dear Justin:
>
> Thank you for your suggestions. using shift for vdwtype helps a lot.
>
> Can I ask you another question? The density of my system is about 8%
> larger than the experimental value. Do you have any suggestions on how
> to reduce the density of the system. Or once the force field and all the
> parameters are fixed, the density is independent of the MD procedure? I
> am using NPT ensemble with the mdp I mentioned before with added vdwtype
> = shift.
>
>
Output like density, pressure, energy conservation, etc. are a consequence of
both the force field parameters and their proper use. Look into the primary
literature for the force field you are using and see how well the parameters are
expected to behave. A difference of 8% doesn't sound that unreasonable to me,
but the primary literature will be the judge.
-Justin
>
> On Thu, May 14, 2009 at 4:35 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Yanmei Song wrote:
>
> Dear Justin:
>
> Thanks for your response. Here is the complete my .mdp file:
>
> title = pdm
> cpp = /lib/cpp
> constraints = all_bonds
> integrator = md
> dt = 0.004 ; ps !
> nsteps = 2500000 ; total 10ns.
> nstcomm = 1
> nstxout = 50000
> nstvout = 50000
> nstfout = 0
> nstlog = 5000
> nstenergy = 5000
> nstxtcout = 25000
> nstlist = 10
> ns_type = grid
> pbc = xyz
> coulombtype = PME
> rlist = 1.4
> rcoulomb = 1.4
> rvdw = 1.4
> fourierspacing = 0.20
> pme_order = 4
> ewald_rtol = 1e-5
> ; Berendsen temperature coupling is on in one groups
> Tcoupl = berendsen
> tc_grps = PDM
> tau_t = 0.1
> ref_t = 300
> ; Energy monitoring
> energygrps = PDM
> ; Isotropic pressure coupling is now on
> Pcoupl = berendsen
> pcoupltype = isotropic
> ;pc-grps = PDM
> 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
>
>
>
> The problem you're seeing could be an artifact of the shorter
> cutoff. Have you tried using DispCorr = EnerPres? Or what about
> using a Shift function for vdwtype? You might see better energy
> conservation in that case compared to a plain cutoff.
>
> -Justin
>
>
> On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Yanmei Song wrote:
>
> Dear All:
>
> I have question about the pressure coupling. I have done
> a 10ns
> simulation with 19800 atoms for 120 large molecules using the
> following pressure coupling.
>
> Tcoupl = berendsen
> tc_grps = PDM
> tau_t = 0.1
> ref_t = 300
>
> Pcoupl = berendsen
> pcoupltype = isotropic
> ;pc-grps = PDM
> tau_p = 1.0
> ref_p = 1.0
> compressibility = 4.5e-5
>
> Then I did g_energy for the last 3ns and got the results:
>
> Energy Average RMSD Fluct.
> Drift Tot-Drift
>
> -------------------------------------------------------------------------------
> Potential -98061 0 0
> 0.61668 1850.04
> Temperature 303.561 109.602 109.602
> 0.000181791 0.545372
> Pressure (bar) 4.4884 11110.8 11109.8
> -0.169835 -509.506
>
> For such a long run the pressure drift is still too much and
> seem hasn't approached 1bar. Does it mean the system hasn't
> reach equilibrium yet. I did a similar system by using
> the same
> method. it just take 2 or 3ns to reach the equilibrium.
> and the
> pressure is around 1.01after the run. The only difference
> is the
> cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4
> is too
> large to make the system running slower. Or the pressure
> coupling method is not working well. Anyone can give me any
> suggestions?
>
>
>
> I think it will depend on the interplay of other parameters
> as well.
> Posting a complete .mdp file may be more helpful.
>
> -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> <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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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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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