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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