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<DIV>In God We Trust<BR>Hello everyone <BR>We have a problem for
equilibrate the system with a protein within <BR>POPE. we have searched
mailing list , we dident any good note. We have used pope.pdb from Dr.
Tielemans website. We have inserted our protein into pope and minimized it
and equilibrated it with NVT ensemble for 2 ns, and temperture was stable,
but when we want to equilibrate our system <BR>with NPT ensemble it dosen't
accept lincs algoritm and says :<BR>" <STRONG>presure coupling more than 1%
</STRONG>" and also "<STRONG> box was shifted at least 10 time</STRONG>.
</DIV>
<DIV>here is our npt file for position reastrant:</DIV>
<DIV>constraints =
all-bonds<BR>
define
= -DPOSRES -DPOSRES_pop<BR>
integrator =
md<BR>
dt
= 0.002; ps <BR>
nsteps
= 2500000; .<BR>
nstcomm
= 1<BR>
comm_mode
= Linear<BR>
comm_grps
= upper lower SOL<BR>
nstxout
= 250<BR>
nstvout
= 1000<BR>
nstfout
= 0<BR>
nstlog
= 10<BR>
nstenergy
= 10<BR>
nstlist
= 1<BR>
ns_type
= grid<BR>
rlist
= 1<BR>coulombtype
= cut-off<BR>
rcoulomb
= 1.4<BR>
rvdw
= 1.4<BR>fourierspacing = 0.12<BR>
fourier_nx =
0<BR>fourier_ny
= 0<BR>
fourier_nz =
0<BR>pme_order
= 4<BR>
ewald_rtol =
1e-5<BR>optimize_fft =
yes<BR>
niter
= 20<BR>
pbc
= xyz <BR>
nstcgsteep
= 1000<BR>
nbfgscorr
= 10<BR>
vdwtype
= cut-off<BR>
DispCorr
= EnerPres<BR>
freezegrps =
Protein<BR>
freezedim
= Y Y Y<BR>
emtol
= 100<BR>
emstep
= 0.01<BR>energygrps =
Protein <BR>energygrp_excl = Protein
Protein<BR>; Berendsen temperature coupling is on in three groups<BR>
Tcoupl
= Nose-Hoover<BR>
tau_t
= 0.1 0.1 0.1 <BR>
tc-grps = Protein POP
bulk <BR>
ref_t
= 100 100
100 <BR>; Pressure coupling
is on<BR>
Pcoupl
= Berendsen <BR>
Pcoupltype =
semiisotropic<BR>
tau_p
= 1 1 <BR>compressibility =
4.5e-05 4.5e-05 <BR>
ref_p
= 1 1 <BR>; Generate velocites is on at 300 K.<BR>
gen_vel
= yes<BR>
gen_temp
= 100.0<BR>
gen_seed
= 173529</DIV>
<DIV>constraint-algorithm =lincs </DIV>
<DIV>lincs_iter = 1<BR>
lincs_order = 4</DIV>
<DIV> </DIV>
<DIV>whould you please gide me</DIV>
<DIV> </DIV>
<DIV>Many thanks in advance for your help and your reply.<BR>Yours truly <BR>
Karim Mahnam<BR>Institute
of Biochemistry and Biophysics (IBB)<BR>
Tehran University <BR>P.O.box 13145-1384<BR>Tehran <BR>Iran <BR>
http://www.ibb.ut.ac.ir/<BR><BR></DIV>
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