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

jampani srinivas jampanis at gmail.com
Fri Feb 26 17:11:04 CET 2010


Hi Berk,

I am extremely sorry, here is the correct log file

++++++++++++++++
grpopts:
   nrdf:           0              0
   ref_t:         300           0
   tau_t:         0.1         0.1
++++++++++++++++

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
> **********************************************
>
>
>
>
> ------------------------------
> 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!
> Please don't post (un)subscribe requests to the list. Use the
> 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
> **********************************************
>
>
>
> ------------------------------
> 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 posting!
> Please don't post (un)subscribe requests to the list. Use the
> 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
> **********************************************
>
>
>
> ------------------------------
> 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 posting!
> Please don't post (un)subscribe requests to the list. Use the
> 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
**********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100226/4942ac3d/attachment.html>


More information about the gromacs.org_gmx-users mailing list