<P>
<BR>
Hi all, <BR>
I have embedded protein into POPC bilayer, I accomplished energy minimisation <BR>
<BR>
em.mdp file<BR>
<BR>
cpp = /usr/bin/cpp<BR>
define = -DFLEXIBLE<BR>
constraints = none<BR>
integrator = steep<BR>
nsteps = 500<BR>
<BR>
; Energy minimizing stuff<BR>
;<BR>
emtol = 100<BR>
emstep = 0.01<BR>
nstcomm = 1.0<BR>
ns_type = grid<BR>
rlist = 1.0<BR>
rcoulomb = 1.0<BR>
rvdw = 1.4<BR>
Tcoupl = no<BR>
Pcoupl = no<BR>
<BR>
its showed following sentences<BR>
<BR>
Stepsize too small, or no change in energy.<BR>
Converged to machine precision,<BR>
but not to the requested precision Fmax < 100<BR>
<BR>
Double precision normally gives you higher accuracy.<BR>
<BR>
writing lowest energy coordinates.<BR>
<BR>
Steepest Descents converged to machine precision in 104 steps,<BR>
but did not reach the requested Fmax < 100.<BR>
Potential Energy = -2.2754422e+05<BR>
Maximum force = 2.3355256e+03 on atom 913<BR>
Norm of force = 9.4749170e+03<BR>
<BR>
gcq#191: "These Gromacs Guys Really Rock" (P.J. Meulenhoff)<BR>
<BR>
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 <BR>
means POPC tails are tilting, water molecules structure also disturbed.<BR>
<BR>
Could you please tell me where iam doing mistake?<BR>
<BR>
my pr.mdp filetitle = protein in popc restrained<BR>
define = -DPOSRES_protein<BR>
constraints = all-bonds<BR>
integrator = md<BR>
dt = 0.002 ; ps !<BR>
nsteps = 10000 ; total 50 ps.<BR>
nstcomm = 1<BR>
nstxout = 50<BR>
nstvout = 1000<BR>
nstfout = 0<BR>
nstlog = 10<BR>
nstenergy = 10<BR>
nstlist = 10<BR>
ns_type = grid<BR>
rlist = 0.9<BR>
coulombtype = PME<BR>
rcoulomb = 0.9<BR>
rvdw = 1.4<BR>
pbc = xyz<BR>
; Berendsen temperature coupling is on in three groups<BR>
Tcoupl = Berendsen<BR>
tc-grps = POPC Protein SOL_CL-<BR>
tau_t = 0.1 0.1 0.1<BR>
ref_t = 310 310 310<BR>
; Anisotropic pressure coupling is now on<BR>
Pcoupl = berendsen<BR>
pcoupltype = anisotropic<BR>
tau_p = 1.0 1.0 1.0 0 0 0<BR>
compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0<BR>
ref_p = 1.0 1.0 1.0 0 0 0<BR>
; Energy monitoring<BR>
energygrps = POPC Protein SOL_CL-<BR>
; Generate velocites is on at 300 K.<BR>
gen_vel = yes<BR>
gen_temp = 310.0<BR>
gen_seed = 173529<BR>
<BR>
Thanks in advance. <BR>
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