hazizian wrote:
Hi
As I told in my perevious mail, My system consist of a 2-domain protein
(Domain A and B), even when I did EM minimization this 2 damain separated.
No they didn't. Check the website.
my em.mpf is:
title = n.pdb
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 40000
constraint_algorithm = shake
shake_tol = 0.0001
nstenergy = 10
nstxtcout = 10
nstlist = 5
ns_type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Energy minimizing stuff
;
emtol = 10.0
emstep = 0.01
Also it is not because of pbc,
What do you suggest for solving this, thank you very much for replying.
--
Tehran University of Medical Sciences
www.tums.ac.ir
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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