[gmx-users] problem with the size of freeze groups
jampani srinivas
jampanis at gmail.com
Wed Mar 3 03:11:06 CET 2010
Dear Berk,
Thanks for your previous responses, Can you please let me know if you have
any solution for the size of freezing groups? I am still not able to do if i
have larger freezing groups.
Thanks again for your kind help.
srinivas.
On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas <jampanis at gmail.com>wrote:
> Dear Berk,
>
> I have checked my inputs and tcl scripts that i have used for
> the selection, i could see that my selection doesn't have any problem.
> I submitted it again still i am getting the same log file with nrdf 0 for
> non-freezing group. Please let me know if you want see any of my input
> files, and help me if you have solution for this problem.
>
> Thanks and Regards
> Srinivas.
>
>
> On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas <jampanis at gmail.com>wrote:
>
>> 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
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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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>>> New Windows 7: Simplify what you do everyday. Find the right PC for you.<http://windows.microsoft.com/shop>
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>>> gmx-users mailing list gmx-users at gromacs.org
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>>> Please search the archive at http://www.gromacs.org/search before
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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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>>> New Windows 7: Find the right PC for you. Learn more.<http://windows.microsoft.com/shop>
>>>
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>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
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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
> **********************************************
>
>
>
--
*********************************************
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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