Hello, everyone.
I have loaded a pdb file of protein complex from Protein Data Bank and put it
into water soltion with pdb2gmx, editconf and genbox.
After 400 steps of energy minimization when the potential energy seems to be
more or less stable, I want to do position restraints. However, it always
failed.
The error info is as follows:
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.000645 (between atoms 13241 and 13242) rms 0.000043
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
13241 13242 31.2 0.1000 0.0999 0.1000
t = 0.002 ps: Water molecule starting at atom 73326 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous
and current coordinates
Large VCM(group System): 0.03330, -0.01095, -0.00024, ekin-cm:
2.20013e+03
The system seems to be exploding. I have tried the follwing parameters and
sadly, none of them works.
nsteps = 200/400/800/1000 steps in em.mdp
dt = 0.002/0.001/0.0002 ps in pr.mdp
tc-grps = Protein SOL or
tc-grps = system in pr.mdp
tau_t = 0.002 0.002 or longer time in pr.mdp
The total charge of the system is -273.000 e and I didn't neutralize it for
some reasons. Does this matter much?
Some files are as follows:
======= *.top =========
.....
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
Protein_C 1
Protein_D 1
Protein_E 1
Protein_F 1
Protein_G 1
Protein_H 1
Protein_I 1
Protein_J 1
Protein_K 1
Protein_L 1
Protein_M 1
Protein_N 1
Protein_O 1
Protein_P 1
Protein_Q 1
Protein_R 1
Protein_S 1
Protein_T 1
Protein_U 1
SOL 151936
======= em.mdp ============
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 1000;
emtol = 1000
emstep = 0.01
nstxout = 50
nstlist = 5
nstcomm = 1
ns_type = grid
rlist = 1.0
coulombtype =PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
========= pr.mdp ===============
cpp = /usr/bin/cpp
define = -DPOSRES
;constraints = none
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 10 ps.
nstcomm = 1
comm_grps = system
nstxout = 100
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 1
ns_type = grid
vdwtype = Cut-off
rlist = 1.0
rvdw = 1.4
;coulombtype=Cut-off
;rcoulomb=2.2
coulombtype = PME
rcoulomb = 1.0
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein SOL
tau_t = 0.002 0.002
ref_t = 300 300
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
===========================
All the best
Ying Ren
2007-11-14
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