[gmx-users] high initial temperature with low ref_T

[Dongsheng Zhang]

Dear Mark,

Do you have any idea what's wrong with my simulation? You can find the
mdp file and the description how I set up my system at the bottom of
this email. 


All the best!


Dongsheng



On Thu, 2006-07-06 at 19:16 -0400, Dongsheng Zhang wrote:
> 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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