[gmx-users] restarting mdrun

[Chandan Choudhury]

Below is my .mdp file. The timestep dt shows as 0.001 ps

title                    = protein
cpp                      = /lib/cpp
; RUN CONTROL
integrator               = md
nsteps                   = 3000000
dt                       = 0.001
; NEIGHBOR SEARCHING
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 0.9
; OUTPUT CONTROL
nstxout                  = 500
nstvout                  = 500
nstxtcout                = 0
nstlog                   = 10
constraints              = all-bonds
nstenergy                = 100
; OPTION FOR ELECTROSTATIC AND VDW
coulombtype              = PME
rcoulomb_switch          = 0
rcoulomb                 = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon_r                = 1
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw_switch              = 0
rvdw                     = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 2.5
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.28
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl                   = V-rescale
tc_grps                  =  SOL Protein Na
tau_t                    =  0.1 0.1 0.1
ref_t                    =  300 300 300
Pcoupl                   = Berendsen
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Tue, Feb 16, 2010 at 11:27 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 17/02/10 04:43, Chandan Choudhury wrote:
>
>> Thanks Justin !!
>> But my state_prev.cpt file shows
>> $gmxcheck -f state_prev.cpt
>>
>> Checking file state_prev.cpt
>>
>> # Atoms  186864
>> Last frame         -1 time 9346.700
>>
>>
>> Item        #frames Timestep (ps)
>> Step             1
>> Time             1
>> Lambda           1
>> Coords           1
>> Velocities       1
>> Forces           0
>> Box              1
>>
>> Here also the time is greater than the .trr file.
>>
>> Cant understand how to overcome it.
>>
>
> Your checkpoint interval need not match your .trr-writing interval - see
> your .mdp file.
>
>
> Mark
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