[gmx-users] NPT simulation with parinello-rahman pressure coupling
Shyno Mathew
sm3334 at columbia.edu
Wed Apr 11 17:15:20 CEST 2012
Dear gromacs users,
I am having some difficulty in setting up an NPT simulation, following are
the issues
1. With Parinello-Rahman coupling, I am getting the error:
Fatal error:
The X-size of the box (4.224258) times the triclinic skew factor (1.000000)
is smaller than the number of DD cells (5) times the smallest allowed cell
size (0.844801)
As mentioned in the archives, initially I thought my system is too small to
split between different processors. When I load the trajectory I can see
that the box is shrinking very fast in the x direction.
I have performed the same run with Berendsen thermostat and it ran fine.
So changing the pcoupling method can cause such a change?
With the berendsen p coupling I have done a benchmark for the system and I
am using the optimum number of processors. Will the change in pcoupling
affects benchmark as well?
some parameters in .mdp file:
integrator = sd
pbc = xyz
rlist = 1.2
coulombtype = PME
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-05
optimize_fft = no
epsilon_surface = 0
ewald_geometry = 3d
rcoulomb = 1.2
vdwtype = Shift
rvdw_switch = 0.9
rvdw = 1.0
epsilon_r = 1
DispCorr = EnerPres
tc-grps = system
tau_t = 2.0
ref_t = 310
pcoupl = Parrinello-Rahman
pcoupltype = anisotropic
nstpcouple = -1
tau_p = 1.0
2. I changed some of the above mentioned parameters, for example vdwtype to
cut-off and DispCorr to energy as shown below:
rlist = 1.0
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
epsilon_r = 1
DispCorr = Ener
Again I get the same error:
Fatal error:
The X-size of the box (5.000070) times the triclinic skew factor (1.000000)
is smaller than the number of DD cells (5) times the smallest allowed cell
size (1.000000)
Also I thought for obtaining more accurate trajectory, I should apply
dispersion corrections for both pressure and energy, is this true?
3. In the mailing list I found that tau_p has to be greater than tau_t to
avoid larger fluctuations and so changed the parameters as shown below,
everything remains same as in question2 except the following:
tau_t = 2.0
ref_t = 310
tau_p = 3.0
Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
Any help will be appreciated,
thanks
--
Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University
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