[gmx-users] constant pressure in NPT simulation

[Lucia Mydlova]

Thank you very much for your helpful advice.

I simulated polymer PMMA with two organic chromophores in NVT ensemble for
2ns and, the same system one more time for 1.5ns
with parameters:
constraints         =  none
integrator          =  md
dt                  =  0.001
nsteps              =  1500000
comm_mode           =  Linear
nstcomm             =  1
nstxout             =  1000
nstvout             =  1000
nstfout             =  1000
nstlog              =  1000
nstenergy           =  1000
nstxtcout           =  1000
xtc_precision       =  1000
pbc                 =  xyz
nstlist             =  1
cutoff-scheme       =  group
ns_type             =  grid
coulombtype         =  Cut-off
vdwtype             =  Cut-off
rlist               =  1.10
rcoulomb            =  1.10
rvdw                =  1.10
tcoupl              =  nose-hoover
tc_grps             =  system
tau_t               =  0.02
ref_t               =  300
nsttcouple          =  1

and now I want to simulate the system in NPT ensemble for different
temperature from 100K up to 700K
integrator          =  md
dt                  =  0.001 ; ps !
nsteps              =  2000000
comm_mode           =  Linear
nstcomm             =  1
nstxout             =  1000
nstvout             =  1000
nstfout             =  1000
nstlog              =  1000
nstenergy           =  1000
nstxtcout           =  1000
xtc_precision       =  1000
nstlist             =  1
cutoff-scheme       =  group
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  Cut-off
vdwtype             =  Cut-off
rlist               =  1.1
rcoulomb            =  1.1
rvdw                =  1.1
tcoupl              =  nose-hoover
tc_grps             =  system
tau_t               =  0.02
ref_t               =  100
Pcoupl              =  Parrinello-Rahman
pcoupltype          =  isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0

The fluctuation of pressure is high in simulations. Should I use the same
barostat for my system?

Lucia


2018-08-03 9:14 GMT+02:00 Lucia Mydlova <lucia.mydlova at gmail.com>:

> Dear all customers.
>
> I have a problem, in my NPT simulations the pressure is not constant and
> the temperature is. Earlier simulation in NVT conditions was ok. I use
> these parameters:
>  tcoupl              =  nose-hoover
> tc_grps             =  system
> tau_t               =  0.002
> ref_t               =  500
> Pcoupl              =  parrinello-rahman
> pcoupltype          =  isotropic
> tau_p               =  1.0
> compressibility     =  4.5e-5
> ref_p               =  1.0
>
> What should I change in the .mpd file?
> Thank you very much.
> Lucia
>