[gmx-users] Pressure coupling

[Matteus Lindgren]

Hi all!

I am quite new to Gromacs and am wondering why I can´t see any box
fluctuations during a NPT run of protein + urea solvent in dodecahedron. In
the energy output file I can see that the Box-X,Y,Z values only fluctuate
<1%. 

However the pressure average is reasonably close to the ref_p value, 1.7
instead of 1.0 during 20ns. Should there not be any box fluctuations with
the parrinello-rahman algorithm? 

 

I use the input settings specified below.

title                    = Dyna

cpp                      = /usr/bin/cpp

constraints              = hbonds

constraint_algorithm     = lincs

lincs_iter               = 1

integrator               = md

dt                       = 0.002

nsteps                   = 8000000

nstxout                  = 4000000

nstvout                  = 3000

nstlog                   = 250

nstenergy                = 250

nstxtcout                = 250

xtc_grps                 = 

energygrps               = Protein      SOL    UREA     CL-

nstlist                  = 5

ns_type                  = grid

rlist                    = 1.1

coulombtype              = PME

rcoulomb                 = 1.1

rvdw                     = 1.4

fourierspacing           = 0.14

pme_order                = 6

optimize_fft             = yes

tcoupl                   = nose-hoover

tc-grps                  = Protein      SOL    UREA     CL-

tau_t                    = 0.5  0.5  0.5   0.0

ref_t                    = 308  308  308   308

Pcoupl                   = parrinello-rahman

tau_p                    = 1.0

compressibility          = 4.5e-5

ref_p                    = 1.0

 

Thank you!

Regards

 

Matteus Lindgren 

Graduate student 

 

Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
Tel: +46 (0)90 786 53 68
e-mail:  <mailto:barbara.addario at chem.umu.se> matteus.lindgren at chem.umu.se

 

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