[gmx-users] problem with the size of freeze groups
jampani srinivas
jampanis at gmail.com
Wed Mar 3 18:56:42 CET 2010
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
> **********************************************
>
>
>
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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
> **********************************************
>
>
>
> ------------------------------
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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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--
*********************************************
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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