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 Titanic.


Accordingly following the suggestions given in the error I tried to solve it with

Following log file and changed,

1.1. -rcon

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 (0.900)

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 parameters)

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 message?*/

/*If any better way of doing so without changing the output please suggest,*/

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 bonds)
lincs_iter         = 1                               ; accuracy of LINCS
lincs_order     = 4

; Neighborsearching
ns_type           = grid
nstlist              = 5

 rlist                = 1.2
rcoulomb        = 1.2
rvdw                = 1.2
; Electrostatics
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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