On 8/19/17 8:23 AM, Alex Mathew wrote:
Dear all,
In order to obtain the PMF diagram of a water molecule through membrane
protein channel, I set up a simulation system and try to run with
pull_coord1_geometry = direction-periodic. To correct te error following
changes are made in the mdp file {error (Can not have dynamic box while
using pull geometry 'direction-periodic' (dim
z))}
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 2.0
But now it shows
Pressure coupling incorrect number of values (I need exactly 2), can
anyone tell me what changes I need to make
The manual tells you what parameters you need to specify for semiisotropic
pressure coupling.
http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#pressure-coupling
-Justin
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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