minnale wrote:
So I dont boughter about those sentences because I confirmed in list
archives that I can proceed further steps and moreover em.gro file is
fine, so I went for restrain, here I am getting abnormal POPC
structure
means POPC tails are tilting, water molecules structure also disturbed.
Could you please tell me where iam doing mistake?
Not really. You haven't told us much. What parameters are you using
(for the protein and the lipids)? How did you insert your protein?
Also realize that 50 ps is *extremely* short in the realm of membrane
protein MD. Even after several hundred picoseconds things may look a
bit strange. Prevailing wisdom is that between 25-30 ns of MD are
required for the lipids to reach equilibrium (although they should look
reasonable after just a few ns, but parameters like area per headgroup
may not level off for a while).
-Justin
my pr.mdp filetitle = protein in popc restrained
define = -DPOSRES_protein
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 10000 ; total 50 ps.
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
pbc = xyz
; Berendsen temperature coupling is on in three groups
Tcoupl = Berendsen
tc-grps = POPC Protein SOL_CL-
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
; Anisotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = anisotropic
tau_p = 1.0 1.0 1.0 0 0 0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p = 1.0 1.0 1.0 0 0 0
; Energy monitoring
energygrps = POPC Protein SOL_CL-
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 310.0
gen_seed = 173529
Thanks in advance.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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