[gmx-users] Re: how to calculate g_sdf and ionic conductivity
naimah haron naimah
cimot_ima98 at yahoo.com
Wed Oct 21 11:15:04 CEST 2009
Dear Mark....
Thanks for your suggestions.
1) Regarding to the g_sdf, the problem is I have 3 groups ( system, cation, anion) in my index file.
But, before using g_sdf, I should have 4 groups. So, how about the last group?
2) When I used g_sdf command ( g_sdf -s topol.tpr -f trj.trr -n index.ndx -r), it mention to select the group for 4 times. My question is, how to select the group?
THANKS
IMA
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Today's Topics:
1. Re: Re: Chloroform (CHCl3) solvent box for G53a5 force field
(Justin A. Lemkul)
2. why are the values of the LJ interaction energy negative and
the values of the Coulomb interaction energy positive between two
group. (Jinyao Wang)
3. Re: why are the values of the LJ interaction energy negative
and the values of the Coulomb interaction energy positive between
two group. (Mark Abraham)
4. Fatal error: 2 particles communicated to PME node 0 are more
than a cell length out of the domain decomposition cell of their
charge group (wuxiao)
5. Re: Fatal error: 2 particles communicated to PME node 0 are
more than a cell length out of the domain decomposition cell of
their charge group (Mark Abraham)
6. g_rdf and number of atoms to include (Enemark Soeren)
7. how to calculate g_sdf and ionic conductivity
(naimah haron naimah)
8. Re: how to calculate g_sdf and ionic conductivity (Mark Abraham)
----------------------------------------------------------------------
Message: 1
Date: Tue, 20 Oct 2009 19:18:05 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5
force field
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4ADE452D.6090602 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Pablo Englebienne wrote:
> Thanks for confirming this, Justin.
>
> I decided not to use the user-contributed CHCl3 box because the topology
> is not consistent with the GROMOS atom types: the CH is united atom
> (although the mass is 12.01100, it should probably be 13.01900?), while
> in G53a5 there are parameters for C, H and Cl. Has someone ever used
> this box successfully?
>
> I was able to equilibrate the box in NVT (100-200ps gives a stable
> simulation), although it exploded at constant pressure. After looking at
> some references on the mailing lists (both GMX and AMBER), I tried
> increasing tau_p from 2.0 to 5.0 and that yielded a stable 100 ps
> simulation, although the system later (continuing for further ~150 ps)
> started to oscillate wildly in temperature and pressure.
>
> What is the effect of increasing tau_p? Besides making the dynamics
> stable, would changing its value affect the outcome of the simulation in
> any other way?
By increasing tau_p you are reducing the stringency of the pressure coupling,
i.e. allowing the system to change a bit more between coordinate scaling. By
decreasing the frequency of coordinate scaling in extremis, you would lose the
benefit of pressure coupling and achieve an NVT ensemble, with the box
dimensions being essentially static. In the case of a tau_p of 2.0 vs. 5.0, you
should not have this problem.
If the provided box uses a united-atom CH, I would suspect it is not suitable
for GROMOS96 parameters, as you have discovered. In all G96 variants, the H is
explicitly represented. You might consider coming up with your own box. Start
with a coordinate file for one molecule, use genconf to generate a box, and
equilibrate.
If you want any further information about diagnosing the current problem,
posting the .mdp file would be helpful.
-Justin
>
> Thanks again!
> _______________________________________________
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>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 2
Date: Wed, 21 Oct 2009 10:18:19 +0800
From: "Jinyao Wang" <wangjy at ciac.jl.cn>
Subject: [gmx-users] why are the values of the LJ interaction energy
negative and the values of the Coulomb interaction energy positive
between two group.
To: "gmx-users" <gmx-users at gromacs.org>
Message-ID: <456090806.02727 at ciac.jl.cn>
Content-Type: text/plain; charset="gb2312"
Hi gmx-users,
I have calculated the interaction energy between two group. But I find that the values of the LJ interaction energy are negative and the values of the Coulomb interaction energy are positive between two group. So I think the LJ interaction is attractive and the Coulomb interaction is repulsive. Is it correct for my consideration of the interaction ?
Jinyao Wang
wangjy at ciac.jl.cn
2009-10-21
------------------------------
Message: 3
Date: Wed, 21 Oct 2009 13:26:22 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] why are the values of the LJ interaction
energy negative and the values of the Coulomb interaction energy
positive between two group.
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4ADE714E.5000704 at anu.edu.au>
Content-Type: text/plain; charset=GB2312
Jinyao Wang wrote:
> Hi gmx-users,
> I have calculated the interaction energy between two group. But I find that the values of the LJ interaction energy are negative and the values of the Coulomb interaction energy are positive between two group. So I think the LJ interaction is attractive and the Coulomb interaction is repulsive. Is it correct for my consideration of the interaction ?
Maybe. That conclusion would assume
a) that you've calculated it correctly,
b) that the model physics is robust with respect to such a decomposition
when it almost certainly wasn't parameterized for such a property, and
c) the decomposed interaction energy means anything.
Mark
------------------------------
Message: 4
Date: Wed, 21 Oct 2009 10:31:49 +0800
From: wuxiao <xiaowu759 at hotmail.com>
Subject: [gmx-users] Fatal error: 2 particles communicated to PME node
0 are more than a cell length out of the domain decomposition cell of
their charge group
To: <gmx-users at gromacs.org>
Message-ID: <BAY131-W17839D5AC63D6A98F4E4ECE9BF0 at phx.gbl>
Content-Type: text/plain; charset="gb2312"
Dear GMXers,
When I perfomed a MD simulation, it always teminated after about 700 ps with the message:
Fatal error: 2 particles communicated to PME node 0 are more than a cell length out of the domain decomposition cell of their charge group
I utilized the GROMACS-4.0.5. I have searched the maillist to find some similar posts but they can not yet cope with this issues. Could you give me some clues, please?
Best wishes,
Chaofu Wu, Dr.
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Message: 5
Date: Wed, 21 Oct 2009 13:58:24 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Fatal error: 2 particles communicated to PME
node 0 are more than a cell length out of the domain decomposition
cell of their charge group
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4ADE78D0.2000304 at anu.edu.au>
Content-Type: text/plain; charset=GB2312
wuxiao wrote:
> Dear GMXers,
> When I perfomed a MD simulation, it always teminated after about 700
> ps with the message:
> /Fatal error: 2 particles communicated to PME node 0 are more than a
> cell length out of the domain decomposition cell of their charge group/
> I utilized the GROMACS-4.0.5. I have searched the maillist to find
> some similar posts but they can not yet cope with this issues. Could you
> give me some clues, please?
Yep. http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Mark
------------------------------
Message: 6
Date: Wed, 21 Oct 2009 13:28:39 +0800
From: "Enemark Soeren" <chees at nus.edu.sg>
Subject: [gmx-users] g_rdf and number of atoms to include
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<C178399C57FF284FA0022B75E348721905E7A9BF at MBX03.stf.nus.edu.sg>
Content-Type: text/plain; charset="us-ascii"
Dear users,
I would like to compare interactions between molecules by using RDF. I
have tried looking at glycine and water, and compare the following two
interactions:
1) between the amine hydrogen atoms in glycine and the oxygen atom
in water
2) between the carboxyl oxygen atoms in glycine and the oxygen atom
in water
However, my result in 1) depends on how many of the 3 hydrogen atoms I
include in the calculations. Why is that? Does that mean that I cannot
directly compare the strengths (RDF peak height) of the two interactions
as they are not based on the same number of atoms? Does it also mean
that I must always calculate RDFs by using 1 atom on each of the
particles/groups that I am comparing?
Thanks,
Soren
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Message: 7
Date: Tue, 20 Oct 2009 23:48:12 -0700 (PDT)
From: naimah haron naimah <cimot_ima98 at yahoo.com>
Subject: [gmx-users] how to calculate g_sdf and ionic conductivity
To: gromacs <gmx-users at gromacs.org>
Message-ID: <662629.64091.qm at web36505.mail.mud.yahoo.com>
Content-Type: text/plain; charset="us-ascii"
Hello all........
Did anyone know how to
1) calculate g_sdf?
2) ionic conductivity?
Can I have the commands for that....
Thanks
IMA
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Message: 8
Date: Wed, 21 Oct 2009 18:20:40 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] how to calculate g_sdf and ionic conductivity
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4ADEB648.1010308 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
naimah haron naimah wrote:
> Hello all........
>
> Did anyone know how to
> 1) calculate g_sdf?
Start with g_sdf -h.
> 2) ionic conductivity?
Don't know. Look in manual 7.4, 8 and maybe Appendix D.
> Can I have the commands for that....
If you do some more of your own work and ask focussed questions you help
yourself look worth helping :-)
Mark
------------------------------
Dear Mark....
Thanks for your suggestions.
1) Regarding to the g_sdf, the problem is I have 3 groups ( system, cation, anion) in my index file.
But, before using g_sdf, I should have 4 groups. So, how about the last group?
2) When I used g_sdf command ( g_sdf -s topol.tpr -f trj.trr -n index.ndx -r), it mention to select the group for 4 times. My question is, how to select the group?
THANKS
IMA
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