[gmx-users] problem with the size of freeze groups
jampani srinivas
jampanis at gmail.com
Fri Apr 2 16:39:34 CEST 2010
Dear Berk,
Sorry to come up with some problems. As I mentioned to earlier, the
simulations were running fine by generating non-zero "ndrf" value for
non-frozen and zero "nrdf" value for frozen atoms. Unfortunately i could see
that there is a continuous increase in the energy of the system. Do i need
to change any parameter in my md.mdp file or something else? I run a short
minimization before submitting production run, energy is converged after
4000 steps and i have taken the same system and applied freezing options and
run the production run. Is there anything wrong in my procedure? can you
please help me to solve this problem?
Thanks very much for your kind help.
Srinivas.
On Wed, Mar 17, 2010 at 8:25 PM, jampani srinivas <jampanis at gmail.com>wrote:
>
> Dear Berk,
>
>
>> Sorry for the delayed reply, We have compiled the gromacs with readir.c
>> that you have sent me, now it is working fine.
>>
>> Thank you very much for your kind help.
>>
>> Srinivas.
>>
>>
>> On Wed, Mar 3, 2010 at 1:56 PM, jampani srinivas <jampanis at gmail.com>wrote:
>
>> Dear Berk,
>>
>> Thanks for your reply, I have just submitted all my files to
>> bugzilla.gromacs.org. I got the bug # 400.
>>
>> Thanks very much
>> Srinivas.
>>
>> On Wed, Mar 3, 2010 at 4:15 AM, Berk Hess <gmx3 at hotmail.com> wrote:
>>
>>> Hi,
>>>
>>> I don't know exactly what you have done, so currently I can say more than
>>> I have done already.
>>>
>>> Could you please file a bugzilla at bugzilla.gromacs.org and attach all
>>> the files required to run grompp?
>>>
>>> Thanks,
>>>
>>> Berk
>>>
>>> ------------------------------
>>> Date: Tue, 2 Mar 2010 21:11:06 -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 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
>>> Mob: 704-706-4191
>>> Web:http://jsrao.web.officelive.com/default.aspx
>>> **********************************************
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>>>
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>>> New Windows 7: Find the right PC for you. Learn more.<http://windows.microsoft.com/shop>
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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: 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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>>>
>>>
>>>
>>> --
>>> *********************************************
>>> 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
>>> **********************************************
>>>
>>>
>>>
>>> ------------------------------
>>> New Windows 7: Simplify what you do everyday. Find the right PC for you.<http://windows.microsoft.com/shop>
>>>
>>> --
>>> 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
>>> **********************************************
>>>
>>>
>>>
>>> ------------------------------
>>> New Windows 7: Find the right PC for you. Learn more.<http://windows.microsoft.com/shop>
>>>
>>> --
>>> 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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>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>> --
>>> *********************************************
>>> 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
>>> **********************************************
>>>
>>>
>>>
>>> ------------------------------
>>> Express yourself instantly with MSN Messenger! MSN Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
>>>
>>> --
>>> 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
>>> posting!
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>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>>
>> --
>> *********************************************
>> 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 Ph.D.
>
> 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, USA.
>
> 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, USA.
Ph: Off: 215-895-1989
Mob: 704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx
**********************************************
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