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

[Berk Hess]

Hi,

It seems there is a bug in grompp, which subtracts degrees of freedom for
constraints in water also for frozen water molecules.
I guess the md.log file reports zero degrees of freedom for your t-coupl group.
You can circumvent this issue by putting all your frozen atoms in a separate
t-coupling group.

Berk

Date: Wed, 24 Feb 2010 21:34:30 -0500
From: jampanis at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] problem with the size of freeze groups

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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