1) I use steepest to minimize energy, .mdp as follows,
title = bovin
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXIBLE
constraints = all-bonds
integrator = steep
dt = 0.002 ; ps !
nsteps = 2000
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep =0.01
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 293
gen-seed = 173529
2) then I use cg do energy minimization, .mdp as follows,
title = bovin
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = all-bonds
integrator = cg
dt = 0.002 ; ps !
nsteps = 1000
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
emtol = 100.0
emstep = 0.01
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 293
gen-seed = 173529
both constraint all bond, 1) steepest is no problem;
but 2) some error take place at cg
I use
grompp_d -f em_cg_constrain.mdp -c em.pdb -p topol.top -o bovin_em_cg.tpr
mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg
Starting 16 threads,
...........
Fatal error:
DD cell 1 4 0 could only obtain 14 of the 16 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order.
at em_cg.log , maximum distance required for P-LINCS: 0.876 nm
So, I revised the mdrun,
mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg -nt 2 -rcon 0.876 nm -dds 0.876
Starting 2 threads,
...........
another error take place,
Fatal error:
Too many LINCS warnings (1011)
If you know what you are doing you can adjust the lincs warning threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
the information on .log :
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.598 nm, LJ-14, atoms 942 950
multi-body bonded interactions: 0.598 nm, Proper Dih., atoms 942 950
Minimum cell size due to bonded interactions: 0.657 nm
User supplied maximum distance required for P-LINCS: 0.876 nm
Using 0 separate PME nodes
Optimizing the DD grid for 2 cells with a minimum initial size of 0.876 nm
The maximum allowed number of cells is: X 7 Y 7 Z 7
Domain decomposition grid 2 x 1 x 1, separate PME nodes 0
PME domain decomposition: 2 x 1 x 1
Domain decomposition nodeid 0, coordinates 0 0 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
Have you tried lowering the starting temperature to that of the model?
This should help
http://comments.gmane.org/gmane.science.biology.gromacs.user/44384
There you have this answer:
"The DD geometry depends upon the configuration of the system, constraints
applied, cutoffs, and any other special restraints (like distance restraints)
that may be present. The error message suggests that you decrease the number of
DD cells, which I would suggest you try. This makes each DD cell larger and
thus capable of handling longer interactions. There are minimum size limits
defined in the log file; if the system changes much then these can become invalid."
Althougth you change the dd value, you do not mention which warnings you obtain in this second case. There are so many...perhaps you have problems with the topology definition.
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