[gmx-users] high initial temperature with low ref_T

[Dongsheng Zhang]

Mark,
Thank you very much for your reply. 

On Fri, 2006-07-07 at 08:51 +1000, Mark Abraham wrote:
> > Hello, GMX users,
> >
> > My system exploded very soon after mdrun. So I outputted the log file
> > every step. I found the initial temperature is about 800 K even though I
> > set ref_T = 300. Why does this happen?
> 
> First please tell us you've done energy minimization and checked the
> structure and resulting trajectory visually to see that things look
> reasonable there. 


The following is the mdp file:

; VARIOUS PREPROCESSING OPTIONS
title                    = nanotube_polymer - z T300
cpp                      = /lib/cpp -traditional
include                  = 
define                   = 


; RUN CONTROL PARAMETERS
integrator               = md
tinit                    = 0              ; Start time and timestep in
ps
;constraints		 = hbonds         ; constrain bonds involving H.
dt                       = 0.002
nsteps                   = 1000000       ;2 ns

comm-mode                = ANGULAR   ;Linear 
nstcomm                  = 1
comm-grps                = 

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
;   this affects file "traj.trr"
nstxout                  = 50000
nstvout                  = 50000
nstfout                  = 50000

; Checkpointing helps you continue after crashes
nstcheckpoint            = 1000

; Output frequency for energies to log file and energy file
nstlog                   = 1
nstenergy                = 1
energygrps		 =  CNT polymer

; Output frequency and precision for xtc file (for the movie)
nstxtcout                = 1
xtc-precision            = 1000


; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 5            ; nblist update frequency
ns_type                  = simple        ; ns algorithm (simple or grid)
pbc                      = no
rlist                    = 0          ; nblist cut-off        


; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics: Cut-off, 
coulombtype              = Cut-off
fourierspacing           = 0.12
pme_order                = 4
rcoulomb                 = 0
optimize_fft		 = yes  ;This saves a few percent for long simulations
;rcoulomb_switch          = 0.95
; Dielectric constant (DC) for cut-off or DC of reaction field
;epsilon-r                = 1.0 ; for reaction field

; Method for doing Van der Waals
vdw-type                 = cut-off
; cut-off lengths       
rvdw                     = 0
;rvdw_switch              = 0.95

; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = no; EnerPres



; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
Tcoupl                   = berendsen  ; nose-hoover ;berendsen
; Groups to couple separately
tc-grps                  = polymer CNT
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1   0.1
ref_t                    = 300   300
; Pressure coupling     
Pcoupl                   =  no;
berendsen     ;Parrinello-Rahman ;berendsen
Pcoupltype               = isotropic 
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 1.0   


; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 1223188

;Electric fields
;E_z = 1 40 1


My system is a carbone nanotube with a polymer. The polymer has 80
units. After I generated the polymer chain, I have relaxed the polymer
alone in vacuum for 200 ps. Then I added CNT to the system, and made
sure there was no overlap by VMD. Then I did EM in vacuum. I used the
above mdp to generate a tpr file. When I ran it, the polymer exploded.
However, If I simulate the polymer alone in vacuum, it works fine with
the same force field. This problem sounds strange to me. How do you
think?


Best Wishes!

Dongsheng



> If so, and there are still problems you'll need to
> supply a full .mdp and describe the simulation you're trying to run.
> 
> Mark
> 
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