[gmx-users] problem with the size of freeze groups
Berk Hess
gmx3 at hotmail.com
Wed Mar 3 10:15:32 CET 2010
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 RegardsSrinivas.
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.
ThanksSrinivas.
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
###############
ThanksSrinivas.
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 againSrinivas.
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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Computational Biophysics Group
Department of Physics
Drexel University
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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.
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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 posting!
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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.
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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 posting!
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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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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