[gmx-developers] EM with gmx4.0.2

[andrea spitaleri]

Hi there,
we having trouble in EM using gmx-4.0.2. Basically the problem is that the run crash immediately
complaining about the number of separate PME:

>mdrun -s box -v -deffnm boxem

Program mdrun, VERSION 4.0.2
Source code file: domdec_setup.c, line: 132

Fatal error:
Could not find an appropriate number of separate PME nodes. i.e. >= 0.727885*#nodes (11) and <=
#nodes/2 (8) and reasonable performance wis
e (grid_x=88, grid_y=88).
Use the -npme option of mdrun or change the number of processors or the PME grid dimensions, see the
manual for details.

while:

>mdrun -s box -npme 8 -v -deffnm boxem
gives:
Program mdrun, VERSION 4.0.2
Source code file: domdec.c, line: 5860

Fatal error:
The size of the domain decomposition grid (0) does not match the number of nodes (8). The total
number of nodes is 16

We are able to minimize the system using gmx-3.3.3 and then run the MD with gmx-4.0.2 without troubles.
our em.mdp is:

define              =  -DFLEXIBLE
integrator          =  steep
dt                  =  0.002    ; ps
nsteps              =  2000
nstlist             =  5
ns_type             =  grid
pbc                 =  xyz
rlist               =  0.9
table-extension     =  2
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.15
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft              =  yes
;
;       Energy minimizing stuff
;
emtol               =  1000
emstep              =  0.01
lincs_iter          = 4


any help is well accepted.

thanks in advance

andrea

-- 
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
-------------------------------