[gmx-users] like position restrains

[Dmitry Kovalsky]

Dear All,

I'm trying to simulate my protein in water with salt using PME
and have encountered a problem.
After position restrained dynamics I performed usual dynamics with PME during 
3 ns. First 500 ps of the simulation I observed something like ordinary 
dynamics but after this ALL of the system atoms became vabrating like in  
position restrain simulation around their positions and there is no any 
collective movements.

here is my mdp file 

cpp                 =  /lib/cpp
constraints         = all-bonds
constraint_algorithm =  lincs
integrator          =  md
dt                  =  0.004
nsteps              =  750000
nstcomm             =  1
nstxout             =  1000
nstvout             =  1000
nstfout             =  1000
coulombtype         =  PME
rcoulomb            =  0.9
rcoulomb_switch     =  0
pme_order           = 4
optimize_fft        = no
fourierspacing      =  0.12
ns_type             =  grid
vdwtype             = Cut-off
rlist               = 0.9
rvdw                = 1.5
nstlist             = 10
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  5402


Is this because of temperature coupling absence?
What I'm duing wrong?

Thank in advance
 
Sincerely yours,

Dima 

Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143
UKRAINE

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589