[gmx-users] Molecular solid NPT simulation problem

[Guilherme Duarte Ramos Matos]

Dear Gromacs users,

I'm currently working with organic molecular solids and I'm trying to
follow the protocol stablished in JCP, 139, 034104 (2013) (DOI:
10.1063/1.4812362). Before a production run in the NVT ensemble to get the
Helmholtz potential for a certain molecular solid, I have to get the
equilibrium box shape of the crystal I have under a certain pressure. I
understand I have to use the anisotropic Parrinello-Rahman pressure
coupling method for this purpose, but I'm facing some problems.

Some important information before stating the problem:


   1. The initial coordinates are already at the minimum energy
   configuration. Each atom is bound to its lattice position by a harmonic
   potential and the initial structure corresponds to a minimum. No charge and
   vdw terms.
   2. A NVT equilibration run works perfectly, with no warnings.


After the submission of the job, when it reaches the NPT simulation the
following error message is printed out:


Fatal error:
Not enough memory. Failed to realloc -201365740 bytes for grid->nra,
grid->nra=0x6eff2010
(called from file
/work/cluster/nate/GROMACS/gromacs-4.6.3/src/mdlib/nsgrid.c, line 492)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Please notice that there is a negative number of bytes and that was new to
me. Changing to the Berendsen barostat I got:


Step 5  Warning: pressure scaling more than 1%, mu: 0.999968 1.00001
0.986164

Step 7  Warning: pressure scaling more than 1%, mu: 1.00043 0.999709 1.57535

Step 8  Warning: pressure scaling more than 1%, mu: 1.00144 0.999821 1.30892

Step 9  Warning: pressure scaling more than 1%, mu: 0.996529 1.00488
-18.9981


The job then would be killed because it exceeded the time it was allowed to
run. Increasing tau_p here produced the same negative memory reallocation
problem. My original mdp file is:


integrator   = md        ;
tinit       = 0          ;
dt          = 0.002      ;
nsteps      = 100000     ;
comm-mode   = none       ;

; Output Control
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 5000
; Output frequency for energies to log file and energy file
nstlog                   = 1000
; Output frequency and precision for xtc file
nstxtcout                = 1000
xtc-precision            = 10000

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 1
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc                      = xyz
; nblist cut-off
rlist                    = 1.0

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
; Method for doing electrostatics
;coulombtype              = PME
coulombtype              = cut-off
rcoulomb                 = 1.0
; Method for doing Van der Waals
vdw-type                 = cut-off
; cut-off lengths
rvdw-switch              = 1.0
rvdw                     = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = AllEnerPres

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl                   = v-rescale
tau_t                    = 2
ref_t                    = 298.15
tc-grps                  = system

; Pressure coupling
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = anisotropic
tau_p                    = 10 10 10 10 10 10
compressibility          = 4.5e-05 4.5e-05 4.5e-05 4.5e-05 4.5e-05 4.5e-05
ref_p                    = 1.01325 1.01325 1.01325 1.01325 1.01325 1.01325
refcoord_scaling         = com

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no
gen_temp                 = 298.15
gen_seed                 = 3414125

; Constraints
constraints              = all-angles
constraint-algorithm      = lincs
lincs-iter                = 4
lincs-order               = 6


I'm relatively new to this kind of simulation and it would be really nice
if someone helped me with it.

Thank you very much!

~ Guilherme

*****************************************************
Guilherme D. R. Matos
Graduate Student at UC Irvine
Mobley Group

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