Fabrizio Marinelli wrote:
Here it is my .mdp file, i attach you also the topology file, just to be
more specific the one that are 0 are the SR interactions, thank you very
much.
For diagnostic purposes, can you re-process your structure using a different
force field and try again? If the energies are still coming up zero, then there
may be something wrong in the code as a whole, otherwise it is specific to the
CHARMM force field. Either way, I'm out of my league on this one :) Maybe a
developer can comment.
-Justin
Fabrizio
title = Teaa MD
cpp = /lib/cpp
include =
integrator = md
comm_mode = Linear
nstcomm = 10
tinit = 0
comm-grps = System
dt = 0.002
nsteps = 6000000
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
; Output frequency for energies to log file and energy file =
nstlog = 500
nstenergy = 500
nstxtcout = 500
xtc-precision = 100000
xtc_grps = System
energygrps = System
pbc = xyz
nstlist = 5
epsilon_r = 1.
ns_type = grid
coulombtype = pme
vdwtype = Cut-Off
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 2.2e-05
epsilon_surface = 0
optimize_fft = yes
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
tcoupl = Berendsen
tc-grps = System
tau_t = 1.0
ref_t = 298
pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 2.5
compressibility = 4.5e-5
ref_p = 1.0
; Dielectric constant of reaction field =
epsilon_rf = 80.0
gen_vel = yes
gen_temp = 298
gen_seed = 173529
constraints = all-bonds
constraint_algorithm = lincs
shake_tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
user1-grps = System
; Non-equilibrium MD stuff =
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration =
Fabrizio Marinelli wrote:
Hi all,
I have downloaded the latest git version of gromacs (yesterday) in which
it is possible to use the charmm27 force field, I constructed the
topology
for my protein using the pdb2gmx program, everything goes ok also with
the
solvation, but then when i run the MD i notice that coulomb and LJ
interaction are 0 and also the protein consequently unfold.
Did any of you found this kind of problem? Could some of you rpopose
eventually a solution?
Can you post your .mdp file?
-Justin
Thanks in advance,
Fabrizio
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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SISSA Webmail https://webmail.sissa.it/
Powered by SquirrelMail http://www.squirrelmail.org/
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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