On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote:
Dear Gromacs Users,
I am using gromacs version is 4.5.3.and running my jobs on single node
with 8 cores.
I have two different systems which contain about 425000 atoms (protein
+ Lipid +SOL) one with bound ligand
and another one unbound protein.I have successfully reached up to
NPT equilibration run step,
It is a poor idea to do equilibration with Parinello-Rahman, which is
unstable when the system is not already close to equilibrium. For some
reason people still do it, despite at least a post per week on this list
suggesting against it, and a warning in the manual. Use Berendsen to fix
the density, then equilibrate further with P-R to get the right ensemble.
now I want to continue the same for production run. Without ligand I
am able to run successfully But the same system with ligand is
crashing with following error-
D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are
are connected via constraints from the neighbouring cells
This probably means your constraint length are too long
compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells or lincs_order.
I'd rather expect your system was blowing up because of the above issue.
Perhaps the suggestion in the error message is not as complete as could
be desired - you have so many atoms per processor that the constraint
length would normally be tiny with respect to the cell size. So I think
the things you have tried below are rearranging the deck chairs on the
Accordingly following the suggestions given in the error I tried to
solve it with
Following log file and changed,
Estimated maximum distance required for p-lincs was 0.877 thus
I increased it to 0.900
then it thrown another error.
The initial cell size (0.877) is smaller than the cell size limit
2 .Then I tried to increase the --dds and --rdd from original values
of 1.25 and 0.623 to 1.30 and 0.670 respectively.
But it does not help and ended with run crash.
/*What I did was logical or I did it wrongly?*/
/*Now can anyone please suggest me the appropriate way to deal with
the problem mentioned above? */
As I want the continuation of the same run without altering the output
after change in the parameters (As I have to compare the output with
unbound protein run thus can't afford change in output with change in
I know that I need to change some of the parameters in .mdp file such as
fourierspacing from 0.16 to 0.12 and on the contrary increase the
pme_order from say 4 to 6.
/*But as asked above by doing so the output will not or will be the
exact continuation run?*/
/*How to increase the ratio of cell size to constrain length per error
/*If any better way of doing so without changing the output please
I am suffering from the same problem since long,
Please help me .Please see the mdp file for the reference.
integrator = md
nsteps = 10000000
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ;
nstvout = 1000 ;
nstxtcout = 1000 ;
nstenergy = 1000 ;
nstlog = 1000 ;
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4
ns_type = grid
nstlist = 5
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
tcoupl = Nose-Hoover
tc-grps = Protein P SOL_NA_CL ;
tau_t = 0.5 0.5 0.5
ref_t = 323 323 323 group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ;
pcoupltype = semiisotropic
tau_p = 2.0 ; time
ref_p = 1.0 1.0 ; reference
compressibility = 4.5e-5 4.5e-5 ;
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no
Thanking in Advance
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