[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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