[gmx-users] problem with the size of freeze groups
jampani srinivas
jampanis at gmail.com
Thu Mar 18 01:25:56 CET 2010
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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>> --
>> *********************************************
>> 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
>> **********************************************
>>
>>
>>
>> ------------------------------
>> 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
>> 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>
>>
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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
>> **********************************************
>>
>>
>>
>> ------------------------------
>> Express yourself instantly with MSN Messenger! MSN Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
>>
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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 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
**********************************************
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