[gmx-users] problem with the size of freeze groups
jampani srinivas
jampanis at gmail.com
Fri Feb 26 16:50:13 CET 2010
HI
Thanks, My log file shows me "nrdf: 0"
###############
grpopts:
nrdf: 0
ref_t: 0
tau_t: 0
###############
Thanks
Srinivas.
On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess <gmx3 at hotmail.com> wrote:
> Hi,
>
> Then I have no clue what might be wrong.
> Have you check nrdf in the log file?
>
> Berk
>
> ------------------------------
> Date: Fri, 26 Feb 2010 09:54:22 -0500
> Subject: Re: [gmx-users] problem with the size of freeze groups
>
> From: jampanis at gmail.com
> To: gmx-users at gromacs.org
>
> Dear Berk,
>
> Thanks for your response, As you mentioned i have separated t-coupling
> group for frozen and non-frozen groups, still the result is same.
> Herewith i am giving my md.mdp file, Can you suggest me if i am missing any
> options in my md.mdp file?
>
> Thanks again
> Srinivas.
>
> md.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 = Tmp2
> freezedim = Y Y Y
> +++++++++++++++++++++++++++++++++++++++++++++++
>
> On Fri, Feb 26, 2010 at 6:25 AM, Berk Hess <gmx3 at hotmail.com> wrote:
>
> 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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> --
> *********************************************
> J. Srinivasa Rao
> Post-doctoral Research Associate
> C/o Prof. Luis R Cruz Cruz
> 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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--
*********************************************
J. Srinivasa Rao
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
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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