[gmx-users] problem with the size of freeze groups

[jampani srinivas]

Dear Gromacs Users,

I would like to compare the diffusion coefficient of water in different
confined spheres with the bulk solvent, I have taken a solvent box of size
7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as
highest spheres. I have not used the pressure coupling for MD, and temp
coupling is applied for freezing and non freezing waters separately. In case
of the bigger sphere (i. e, 35 Å) the diffusion coefficient is 2.4 10-5
cm2/s (comparable with bulk), but the system with 25 Å radius gives me
almost 0 diffusion coefficient. When I open the log file of 25 Å system it
shows the initial temperature as zero.

Is there any relation between size of freezing group and temperature
coupling? How the sphere with 35 Å radius is working fine but not with the
radius 25 Å?

Can anybody help me?

Here is my m.mdp file

+++++++++++++++++++++++++++++++++++++++++++++++++++++++
title           = AB2130
cpp             = /usr/bin/cpp
constraints     = all-bonds
integrator      = md
dt              = 0.002 ; ps !
nsteps          = 1500000 ; total 3.0 ns.
nstcomm         = 1
nstxout         = 1000 ; collect data     every 2.0 ps
nstvout         = 1000 ; collect velocity every 2.0 ps
nstfout         = 0
nstlog          = 0
nstenergy       = 1000 ; collect energy   every 2.0 ps
nstlist         = 10
ns_type         = grid
rlist           = 1.0
coulombtype     = PME
rcoulomb        = 1.0
rvdw            = 1.0
rvdw_switch     = 0.9
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl          = V-rescale
tau_t           = 0.1  0.1
tc-grps         = Tmp1 Tmp2
ref_t           = 300  0
gen_vel         = yes
gen_temp        = 300.0
acc_grps        = Tmp2
accelerate      = 0.1 0.1 0.1
gen_seed        = 173529
freezegrps      = Freez
freezedim       = Y Y Y
+++++++++++++++++++++++++++++++++++++++++++++++++++++++

-- 
*********************************************
J. Srinivasa Rao
Post-doctoral Research Associate
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104
Ph:  Off:     215-895-1989
       Mob:  704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx
**********************************************
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