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

jampani srinivas jampanis at gmail.com
Fri Feb 26 17:53:49 CET 2010


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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