[EMAIL PROTECTED] wrote:
Dear gmx users,
When I am minimizing a trimer protein in vacuum by SD as well as CG methods,
one of the monomer gets apart from the rest of the protein and places itself
away from the other two monomers, which are intact. No periodic box is
assigned. But when I am running editconf and assigning a box, then the
structures are intact. What is the reason for the above behaviour?
I am pasting the em.mdp below:
chekc your mdout.dmp, the default pbc = xyz
cpp = /lib/cpp
define = -DFLEX_SPC
constraints = none
;integrator = CG
integrator = steep
nsteps = 1000
;
; Energy minimizing stuff
;
emtol = 100
;for SD
emstep = 0.1
;for CG
;emstep = 0.001
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb= 1.0
rvdw= 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
Anwar
--
Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Nacharam
Hyderabad-500 076
INDIA.
Tel: +91-8413-235467,68,69,70 ext 2019
[EMAIL PROTECTED]
---
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--
David.
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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