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

jampani srinivas jampanis at gmail.com
Fri Feb 26 18:39:32 CET 2010


Dear Berk,

I am using VERSION 4.0.5. As you said if there is no problem i should get it
correctly, i don't know where it is going wrong. I have written a small
script in tcl to use in vmd to get my selections. i will check the script
and the selection again. I will let you know my results again.

Thanks for your valuable time and kind help.
Srinivas.

On Fri, Feb 26, 2010 at 12:29 PM, Berk Hess <gmx3 at hotmail.com> wrote:

>  Hi,
>
> Which version of Gromacs are you using?
> I can't see any issues in the 4.0 code, but some older version might have
> problems.
>
> Berk
>
> ------------------------------
> Date: Fri, 26 Feb 2010 12:05:56 -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,
>
> They are same, freeze and Tmp2 are exactly the same groups. I just put them
> like that for my convenience, just to avoid confusion in my second email i
> made it uniform.
>
> Thanks
> Srinivas.
>
> On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess <gmx3 at hotmail.com> wrote:
>
>  That is what I suspected, by I don't know why this is.
>
> Are you really sure you made a temperature coupling group
> that is exactly the freeze group?
> This first mdp file you mailed had a different group names for the freeze
> group
> and the tcoupl groups.
>
> Berk
>
> ------------------------------
> Date: Fri, 26 Feb 2010 11:53:49 -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,
>
> It looks to me some thing is wrong when i change the radius from 35 to 25,
>  herewith i am giving grpopts for both systems
>
>
> +++++++++++++++++++++++++
> grpopts: (system with 35 A)
>    nrdf:     33141.4         0
>    ref_t:         300           0
>    tau_t:         0.1         0.1
> +++++++++++++++++++++++++
>
> grpopts: (system with 25A)
>    nrdf:           0              0
>    ref_t:         300           0
>     tau_t:         0.1         0.1
> ++++++++++++++++++++++++
>
>    I think some thing is going wrong when the size of freezing group is
> increased. I don't know whether my understand is correct or not.
>
>
>
> Thanks
> Srinivas.
>
>
> On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess <gmx3 at hotmail.com> wrote:
>
>  Ah, but that does not correspond to the mdp options tou mailed.
> Here there is only one group with 0 degrees of freedom and reference
> temperature 0.
>
> Berk
>
> ------------------------------
> Date: Fri, 26 Feb 2010 10:50:13 -0500
>
> Subject: Re: [gmx-users] problem with the size of freeze groups
> From: jampanis at gmail.com
> To: gmx-users at gromacs.org
>
> 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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> --
> *********************************************
> 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
> **********************************************
>
>
>
>
>
> --
> *********************************************
> 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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-- 
*********************************************
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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