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

[#ZHANG HAIPING#]

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



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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