[gmx-users] 答复: the water box become much larger in high temporature replicas after replica exchange simulation

[Mark Abraham]

On Jun 5, 2014 1:11 PM, "#ZHANG HAIPING#" <HZHANG020 at e.ntu.edu.sg> wrote:
>
> Dear Mark:
> Thanks for your reply. I plan to used the nvt to run the system again,
because the npt as I mention is low replica rate and low speed, and I
wonder whether the big volume would influence is replica rate.

Indirectly, yes.

> But if I used nvt I have no ideal How many replicas should I use?

Shameless plug: http://pubs.acs.org/doi/abs/10.1021/ct800016r

Mark

>
>
> Best regards,
> Haiping Zhang
> ________________________________________
> 发件人: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
gromacs.org_gmx-users-bounces at maillist.sys.kth.se> 代表 Mark Abraham <
mark.j.abraham at gmail.com>
> 发送时间: 2014年6月5日 16:06
> 收件人: Discussion list for GROMACS users
> 主题: Re: [gmx-users] the water box become much larger in high temporature
replicas after replica exchange simulation
>
> On Jun 5, 2014 8:34 AM, "#ZHANG HAIPING#" <HZHANG020 at e.ntu.edu.sg> wrote:
> >
> > Dear gromacs user：
> >
> > I have used follow .mdp to run the replica exchange simulation, after
the
> simulation, I find the water box become much larger in high temporature
> replicas, can anyone tell me how to solve this? By the way, is it caused
by
> the water box not large enough?
>
> You can't expect constant volume from a constant-pressure ensemble! PV =
nRT
>
> Mark
>
> > title       =  replica exchange MD simulation
> > ; Run parameters
> > integrator  = md        ; leap-frog integrator
> > nsteps      = 500000    ;
> > dt          = 0.002     ; 2 fs
> > ; Output control
> > nstxout     = 0         ; suppress .trr output
> > nstvout     = 0         ; suppress .trr output
> > nstenergy   = 1000      ; save energies every 2 ps
> > nstlog      = 1000      ; update log file every 2 ps
> > nstxtcout   = 3000      ; write .xtc trajectory every 2 ps
> > energygrps  = Protein
> > ; Bond parameters
> > continuation    = yes           ; first dynamics run
> > constraint_algorithm = lincs    ; holonomic constraints
> > constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> > lincs_iter      = 1             ; accuracy of LINCS
> > lincs_order     = 4             ; also related to accuracy
> > ; Neighborsearching
> > ns_type     = grid      ; search neighboring grid cells
> > nstlist     = 5         ; 10 fs
> > rlist       = 1.0       ; short-range neighborlist cutoff (in nm)
> > rcoulomb    = 1.0       ; short-range electrostatic cutoff (in nm)
> > rvdw        = 1.0       ; short-range van der Waals cutoff (in nm)
> > ; Electrostatics
> > coulombtype     = PME       ; Particle Mesh Ewald for long-range
> electrostatics
> > pme_order       = 4         ; cubic interpolation
> > fourierspacing  = 0.16      ; grid spacing for FFT
> > ; Temperature coupling
> > tcoupl      = V-rescale                     ; modified Berendsen
> thermostat
> > tc-grps     = Protein Non-Protein    ; two coupling groups - more
accurate
> > tau_t       = 0.1   0.1                     ; time constant, in ps
> > ref_t       = 587.72   587.72                     ; reference
> temperature, one for each group, in K
> > ; Pressure coupling
> > pcoupl      = Parrinello-Rahman             ; pressure coupling is on
for
> NPT
> > pcoupltype  = isotropic                     ; uniform scaling of box
> vectors
> > tau_p       = 2.0                           ; time constant, in ps
> > ref_p       = 1.0                           ; reference pressure, in bar
> > compressibility = 4.5e-5                    ; isothermal compressibility
> of water, bar^-1
> > ; Periodic boundary conditions
> > pbc         = xyz       ; 3-D PBC
> > ; Dispersion correction
> > DispCorr    = EnerPres  ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel     = no        ; assign velocities from Maxwell distribution
> >
> >
> >
> >
> >
> > best regards,
> >
> > Haiping
> >
> > --
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