[gmx-users] Gromacs versions 4.0.5 and 4.5.4

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 20 00:19:24 CEST 2011


On 20/10/2011 8:40 AM, Sapna Sarupria wrote:
> Hello,
>
> I did change nsttcouple and nstpcouple but the simulations that run in 
> 4.0.5 are still crashing in 4.5.4. I think it is related to 
> constraints but I am unable to figure out exactly what is different. I 
> have pasted both my topology and mdp (updated for 4.5.4) files. Any 
> ideas? I have read through the manual and it seems like the mdp files 
> does not need any changes, but perhaps I am missing something.

P-R P-coupling is not well-suited to equilibration if you are not close 
to equilibrium. Since you are generating velocities, you are likely not 
close to equilibrium.

I don't see that it is causing a problem, but there is no reason to have 
both SOL and TIP molecule type. They're identical.

Mark

>
> Thank you for your help!
>
> Sincerely,
> Sapna
>
> @@@@ MDP File @@@@
> title               =  100% occupancy CO2 hydrate ; a string
> cpp               =  /lib/cpp                 ; c-preprocessor
> integrator        = md
> dt                  =  0.002                    ; time step
> nsteps           =  15000000                 ; number of steps
> nstcomm       =  10                       ; reset c.o.m. motion
> nstxout           =  0000                    ; write coords
> nstvout           =  0000                    ; write velocities
> nstlog             =  25000                    ; print to logfile
> nstenergy       =  500                      ; print energies
> xtc_grps         =  OW_HW1_HW2_CO2
> nstxtcout        =  1000
> nstlist             =  10                       ; update pairlist
> ns_type            =  grid                     ; pairlist method
> coulombtype    =  PME
> rvdw                =  1.2                      ; cut-off for vdw
> rcoulomb         =  1.2                      ; cut-off for coulomb
> rlist                  =  1.2                      ; cut-off for coulomb
> DispCorr         =  EnerPres
> Tcoupl             =  Nose-Hoover
> ref_t                 = 270
> tc-grps             =  System
> tau_t                 =  0.5
> nsttcouple          =  1
> Pcoupl              =  Parrinello-Rahman
> Pcoupltype        =  semiisotropic            ; pressure geometry
> tau_p                  =  1.0   1.0                ; p-coupoling time
> compressibility   =  4.5e-5  4.5e-5           ; compressibility
> ref_p                   =  30.5  30.5               ; ref pressure
> nstpcouple          =  1
> gen_vel               =  yes                      ; generate initial vel
> gen_temp            =  260                      ; initial temperature
> gen_seed             =  372340                   ; random seed
> constraint_algorithm = shake
> constraints         =  all-bonds
> @@@@ end MDP File @@@@
>
> @@@@ Topology file @@@@
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>   1             2               no              1.0     1.0
>
> [ atomtypes ]
> ; name      mass      charge    ptype         sigma       epsilon
> ; Water parameters are those of Vega TIP4P/Ice Model
>  OWT4     15.9994      0.0000    A          0.31668     0.882164429
>   HW        1.008          0.5897    A          0.000       0.000
>   MW        0.000         -1.1794    V          0.000       0.000
>
>
> ; TraPPE  rigid
>   M2      22.0000       0.00      A          0.000      0.000000 ;
>   M1      22.0000       0.00      A          0.000      0.000000 ;
>   DO      00.0000      -0.35      V          0.305      0.656806 ; oxygen
>   DC      00.0000       0.70      V   0.280      0.224478 ; carbon
>
>
> [ moleculetype ]
> ; molname  nrexcl
>   SOL       2
>
> [ atoms ]
> 1       OWT4      1      SOL      OW     1       0.0000
> 2         HW      1       SOL     HW1     1       0.5897
> 3         HW      1       SOL     HW2     1       0.5897
> 4         MW      1       SOL      MW     1      -1.1794
>
> [ bonds ]
> ; ijfunctlengthforce.c.
> 121  0.09572     502416.0
> 131        0.09572     502416.0
> 2       3       1       0.15139     502416.0
>
> [ exclusions ]
> 1    2    3     4
> 2    1    3     4
> 3    1    2     4
> 4    1    2     3
>
> ; The position of the dummy is computed as follows:
> ;
> ;O
> ;
> ;D
> ;
> ;HH
> ;
> ; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
> ; 0.01577 nm/ [ cos (52.26 deg)* 0.09572 nm]
>
> ; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
>
> [ virtual_sites3 ]
> ; Dummy fromfunctab
> 412310.13458335087   0.13458335087
>
> [ moleculetype ]
> ; molname  nrexcl
>   TIP       2
>
> [ atoms ]
> 1       OWT4      1     TIP      OW     1       0.0000
> 2         HW      1       TIP     HW1     1       0.5897
> 3         HW      1       TIP     HW2     1       0.5897
> 4         MW      1       TIP      MW     1      -1.1794
>
> [ bonds ]
> ; ijfunctlengthforce.c.
> 121  0.09572     502416.0
> 131        0.09572     502416.0
> 2       3       1       0.15139     502416.0
>
> [ exclusions ]
> 1    2    3     4
> 2    1    3     4
> 3    1    2     4
> 4    1    2     3
>
> [ virtual_sites3 ]
> ; Dummy fromfunctab
> 412310.13458335087   0.13458335087
>
>
> [ moleculetype ]
> ; molname  nrexcl
>   CO2    2
>
> [ atoms ]
> 1         M1      1       CO2      M1      1       0.00    22.00
> 2         M2      1       CO2      M2      1       0.00    22.00
> 3         DC      1       CO2      CO      1       0.70    0.000
> 4         DO      1       CO2      OC1     1      -0.35    0.000
> 5         DO      1       CO2      OC2     1      -0.35    0.000
>
>
> [ constraints ]
> 1    2      1    0.19785026
>
>
> [ virtual_sites2 ]
> ; ai     aj     ak    funct    a
>   3      1      2     1       0.50
>   4      1      2     1      -0.086327900
>   5      1      2     1       1.086327913
>
> [ exclusions ]
> 3       4       5
> 4       5       3
> 5       4       3
>
> [ system ]
> Hydrate with cages filled with carbon dioxide
>
> [ molecules ]
> SOL    2944
> CO2    512
> TIP    3641
>
> @@@@ End topology file @@@@
>
>

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