Thank you very much,
It worked with NVT, but the water molecule is not going though the channel
at 0.01 nm per ns but It worked when i increased the pull_coord1_rate to
0.5 nm per ns from 0.01nm per ns but could not get proper histogram and
energy profile. What parameters i need to change in
The error is actually telling you exactly what is wrong.
First relax your system with pressure coupling, then do pull in NVT. Or,
possibly adjust the system in such a way that 'direction' pull could be
used instead of 'direction-periodic'.
Alex
On 8/20/2017 1:53 AM, Alex Mathew wrote:
Dear Justin,
As per the manual i have changed parameters as
tcoupl = berendsen
tc_grps = Protein Non-Protein Chain_B
tau_t = 1.01.01.0
ref_t = 310 310 310
;
pcoupl = berendsen
pcoupltype
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
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
