[gmx-users] Re: Constraints - PMF - Different Molecules (Mark Abraham)
Eudes Fileti
fileti at ufabc.edu.br
Sun Nov 16 13:19:02 CET 2008
Hello Mark, thanks for your attention.
I had already made some attempts setting the two molecules
in the same block (as suggested in the forum) but I had no success.
I tried to use restraints and constraints and but run always fails.
Please I am sending my .mdp and .top files as well as the error
message that I getting. Note, there is no bonded parameters molecules
between two molecules.
Can you help me to solve this problem?
>>>>> .mdp file
cpp =
integrator = md
tinit = 0.0
dt = 0.01
nsteps = 10000
nstcomm = 1
nstxout = 1000
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000 # with 1000 we get 10000/1000 == 10 (+ original,
t=0) frames
xtc_precision = 1000
nstlist = 10
energygrps =
ns_type = grid
rlist = 0.9
coulombtype = cut-off
rcoulomb = 0.9
rvdw = 0.9
Tcoupl = Berendsen
tc_grps = system
ref_t = 90
tau_t = 0.2
Pcoupl = No
tau_p = 1.0
compressibility = 1e-4
ref_p = 1.0
gen_vel = yes
gen_temp = 90
gen_seed = 173529
free-energy = yes
init-lambda = 0.96
delta-lambda = -.000064 # in order to get down to .32 nm with 10000 steps
>>>>
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
BEN 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_075 1 BEN C1 1 0 13.019 ; qtot
0
2 opls_075 1 BEN C2 2 0 13.019 ; qtot
0
3 opls_075 1 BEN C3 3 0 13.019 ; qtot
0
4 opls_075 1 BEN C4 4 0 13.019 ; qtot
0
5 opls_075 1 BEN C5 5 0 13.019 ; qtot
0
6 opls_075 1 BEN C6 6 0 13.019 ; qtot
0
7 opls_075 2 BEN C1 7 0 13.019 ; qtot
0
8 opls_075 2 BEN C2 8 0 13.019 ; qtot
0
9 opls_075 2 BEN C3 9 0 13.019 ; qtot
0
10 opls_075 2 BEN C4 10 0 13.019 ; qtot
0
11 opls_075 2 BEN C5 11 0 13.019 ; qtot
0
12 opls_075 2 BEN C6 12 0 13.019 ; qtot
0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
1 6 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
2 3 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
3 4 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
4 5 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
5 6 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
7 8 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
7 12 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
8 9 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
9 10 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
10 11 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
11 12 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
2 5 1
3 6 1
7 10 1
8 11 1
9 12 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 6 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
1 2 3 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
2 3 4 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
3 4 5 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
4 5 6 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
1 6 5 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
8 7 12 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
7 8 9 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
8 9 10 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
9 10 11 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
10 11 12 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
7 12 11 1 1.200000e+02 4.000000e+02 1.200000e+02
4.000000e+02
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
6 1 2 3 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
2 1 6 5 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
1 2 3 4 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
2 3 4 5 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
3 4 5 6 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
4 5 6 1 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
12 7 8 9 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
8 7 12 11 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
7 8 9 10 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
8 9 10 11 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
9 10 11 12 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
10 11 12 7 3 1.800000e+02 5.000000e+00 3.000000e+00
1.800000e+02 5.000000e+00 3.000000e+00
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
7 1 1000 1000 1000
;[ constraints ]
; ai aj ft A B
; 1 7 2 0.0 1.0
[ system ]
; Name
BEN
[ molecules ]
; Compound #mols
BEN 1
>>> Error mensage
Back Off! I just backed up dgdl.xvg to ./#dgdl.xvg.2#
starting mdrun 'BEN'
10000 steps, 100.0 ps.
Back Off! I just backed up traj.trr to ./#traj.trr.3#
Back Off! I just backed up traj.xtc to ./#traj.xtc.2#
Warning: 1-4 interaction between 1 and 4 at distance 419.707 which is larger
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
_______________________________________
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170 Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/ <http://cromo.ufabc.edu.br/%7Efileti/>
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