On 8/6/18 9:07 AM, Lucia Mydlova wrote:
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
A plain cutoff for electrostatic interactions is horribly inaccurate and
not generally viewed as acceptable for modern simulations.
-Justin
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.mydl...@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
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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