[EMAIL PROTECTED] wrote:
Dear all,
I am simulating a protein containing 2 domains which are linked together
by a loop of around 10 residues. When I am simulating the same in vacuum,
after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms
with in 10 time steps. You can surely imagine how drastic the structural
changes are happening. And also during the simulation after 500ps the protein
started to rotate and later at approx 2ns the protein stopped rotation.
What exactly might be happening there, why the protein is behaving like
that. I am pasting the mdp file below.
As Gerrit said, remove pressure coupling in vacuo and remove angular
center of mass motion.
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
title = Yo
cpp = /lib/cpp
constraints = all-bonds
;define = -DPOSRES
integrator = md
dt = 0.002 ; ps !
nsteps = 10000000 ; total 10000 ps.
nstcomm = 1
nstxout = 500
nstvout = 500
nstfout = 500
nstlog = 500
nstenergy = 500
nstlist = 10
ns_type = grid
rlist = 0.9
rcoulomb = 0.9
rvdw = 0.9
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein
tau_t = 0.1
ref_t = 300
; Energy monitoring
energygrps = Protein
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 300 K.
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
kindly guide me in this issue.
regards
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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