[gmx-users] box size changing during isotropic pressure coupling

Chris Neale chris.neale at utoronto.ca
Fri Jul 18 19:54:19 CEST 2008


I have a system of 750,000 atoms consisting of detergent in water. 
Although this run has been carried out using isotropic pressure 
coupling, I see significant drift in the box dimensions over 150 ns. 
This run was carried out using gromacs version 3.3 and 3.3.1. I used the 
-shuffle and -sort options and an in-house g_desort. This means that my 
restarts are via grompp, not tpbconv, although I do use the .trr and 
.edr with gen_vel=no and unconstrained-start=yes for a proper restart.

My system is rectangular, starting with an x=y!=z and a=b=c=90. When I 
view the .xtc file, it is clear that the system is shrinking in the x/y 
and growing in the z. However, while turning on PBC images it looks like 
a totally normal simulation in that there is no net drift or anything 
else obviously problematic.

I have posted some images here 
http://www.pomeslab.com/CN_GromacsPost_071808.html that show the box 
dimensions over time and also the total volume. The initial rapid volume 
change, and its asymptotic continuation, is an aggregation effect and is 
expected. Other than this, the volume is generally stable to the changes 
in the box lengths along single dimensions. I can not explain any of the 
features of the individual x/y/z plots, nor can I explain why they level 
out, why y levels out before x and z, or guess if this will continue to 
stay (relatively) flat.

I am interested to know if anybody else has experienced this. Also, it 
seems to me like this is simply an output format thing and will not 
cause problems unless the x/y shrinks so much that cutoff effects cause 
me problems.

my .mdp file follows.

title               =  seriousMD
cpp                 =  cpp
integrator          =  md
nsteps              =  25000
tinit               =  153200
dt                  =  0.002
comm_mode           =  linear
nstcomm             =  1
comm_grps           =  System
nstxout             =  25000
nstvout             =  25000
nstfout             =  25000
nstlog              =  5000
nstlist             =  10
nstenergy           =  500
nstxtcout           =  5000
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
rcoulomb            =  0.9
fourierspacing      =  0.12
pme_order           =  4
vdwtype             =  cut-off
rvdw_switch         =  0
rvdw                =  1.4
rlist               =  0.9
DispCorr            =  no
Pcoupl              =  Berendsen
pcoupltype          =  isotropic
compressibility     =  4.5e-5
ref_p               =  1.
tau_p               =  4.0
tcoupl              =  Berendsen
tc_grps             =  DPC     SOL
tau_t               =  0.1     0.1
ref_t               =  300.    300.
annealing           =  no
gen_vel             =  no
unconstrained-start =  yes
gen_temp            =  300.
gen_seed            =  9896
constraints         =  all-bonds
constraint_algorithm=  lincs
lincs-iter          =  1
lincs-order         =  4


many thanks,

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