Den 2018-08-14 kl. 16:07, skrev Pelin S Bulutoglu:
Dear GROMACS users,
I am working on simulating a glycine crystal using GAFF force field with CNDO
point charges in an NPT ensemble. I want to calculate the enthalpy and Cp of
the crystal. However, the list that comes up following gmx energy command does
not include the enthalpy or PV options, as it would normally do for NPT
simulations. Does this mean that the simulation does not exhibit NPT behavior?
I believe that this is not the case, since upon inspection of the temperature
and pressure values, I found that they are both constant (within statistical
error) throughout the simulation. What may be the cause of this? The following
are some of my input parameters:
cutoff-scheme = Verlet
nstlist = 40
ns-type = Grid
pbc = xyz
verlet-buffer-tolerance = 0.005
rlist = 1.4
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1.4
rvdw = 1.4
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.12
pme-order = 4
tcoupl = V-rescale
nsttcouple = 10
pcoupl = Berendsen
pcoupltype = Anisotropic
nstpcouple = 10
tau-p = 2
compressibility (3x3):
compressibility[ 0]={ 4.50000e-05, 4.50000e-05, 4.50000e-05}
compressibility[ 1]={ 4.50000e-05, 4.50000e-05, 4.50000e-05}
compressibility[ 2]={ 4.50000e-05, 4.50000e-05, 4.50000e-05}
ref-p (3x3):
ref-p[ 0]={ 1.00000e+00, 1.00000e+00, 1.00000e+00}
ref-p[ 1]={ 1.00000e+00, 1.00000e+00, 1.00000e+00}
ref-p[ 2]={ 1.00000e+00, 1.00000e+00, 1.00000e+00}
refcoord-scaling = COM
Any input would be greatly appreciated. Thanks in advance.
Pelin Su Bulutoglu
The enthalpy should be there with any modern gromacs version if you are
using constant pressure simulations. Please double check gmx energy
options. Cp is more tricky because you need quantum corrections.
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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