[gmx-users] g_nmeig_d error: can't allocate region

[sarbani chattopadhyay]

Hi,
  I am trying to do normal mode analysis on a protein having 6398 atoms in vaccum.

I tried to energy minimize the structure using steepest descent, followed by "l-bfgs" 
minimization. the .mdp file I used is

define                   = -DFLEXIBLE
constraints              = none
integrator               = l-bfgs
tinit                    = 0
nsteps                   = 15000
nbfgscorr                = 50
emtol                    = .001
emstep                   = 0.1
gen_vel                  = yes
gen-temp                 = 300
nstcomm                  =  1
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 0
; ns algorithm (simple or grid)
ns-type                  = simple
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc                      = no
; nblist cut-off
rlist                    = 0
domain-decomposition     = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = Cut-Off
rcoulomb-switch          = 0
rcoulomb                 = 0
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r                = 1
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 0


after running the 15000 steps the Fmax was:
Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 10197 steps
Potential Energy  = -8.26391832320506e+04
Maximum force     =  9.37558560558845e-04 on atom 4562
Norm of force     =  2.24887722104890e-04


Again the "l-bfgs" minimization was run using the same .mdp file( with emtol = 0.000001)

the output was'
Low-Memory BFGS Minimizer converged to Fmax < 1e-06 in 4143 steps
Potential Energy  = -8.26391832324998e+04
Maximum force     =  9.67927896882578e-07 on atom 3271
Norm of force     =  1.70637151528245e-07



After this I prepared the "nm.mdp " file for NMA, where I used exactly the same parameters 
as the ones used in lbfgs energy minimization( with integrator = nm)

the commands that were used were:
grompp_d -f new_nm.mdp -t new_lbfgs_2.trr -c new_lbfgs_2.gro -o new_nm.tpr -zero -p 
../topol.top

nohup mdrun_d -v -s new_nm.tpr -deffnm new_nm -mtx new_nm.mtx &


"nohup.out" had the following message:
Non-cutoff electrostatics used, forcing full Hessian format.Allocating Hessian 
memory...starting normal mode calculation 'Protein'6398 steps.Maximum force: 9.67928e-
07


The run ended successfully:

Then i used the command 
g_nmeig_d -f new_nm.mtx -s new_nm.tpr -ol eigenvalue.xvg -v eigenvector.trr

I get the following error:
Reading file new_nm.tpr, VERSION 4.0.7 (double precision)
Reading file new_nm.tpr, VERSION 4.0.7 (double precision)
Reading double precision matrix generated by Gromacs VERSION 4.0.7
Full matrix storage format, nrow=19194, ncols=19194

Diagonalizing to find vectors 1 through 50...
g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

I am not being able to understand the problem. the computer  has a 16gb memory



If I use different parameters in the nm.mdp file as

rlist                    = 1.5
domain-decomposition     = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = switch
rcoulomb-switch          = 1
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r                = 1
; Method for doing Van der Waals
vdw-type                 = switch
; cut-off lengths
rvdw-switch              = 1
rvdw                     = 1.2


then i get the message :Maximum force: 3.14171e+03
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.


I am sorry to post such a lengthy  query, but I have no clue about the root of the problem.
Any suggestion  will be of great help.
Thanks in advance,
Sarbani. 
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