[gmx-users] gromacs.org_gmx-users Digest, Vol 123, Issue 139
Cyrus Djahedi
cyrusdja at kth.se
Fri Aug 1 15:25:50 CEST 2014
Hi. Im interested in creating an angle group for a characteristic glucosidic angle between two carbon atoms around a central oxygen atom that link glucose units in cellulose. I have simulated fibrils containing 320 of those bonds.
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Skickat: den 25 juli 2014 13:48
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Ämne: gromacs.org_gmx-users Digest, Vol 123, Issue 139
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Today's Topics:
1. Re: Groups in index.ndx (Justin Lemkul)
2. Re: Angle group (Justin Lemkul)
3. hints for core/shell optimization? (Tamas Karpati)
4. Lennard jones parameters for ions (#SUKRITI GUPTA#)
5. Lennard jones parameters for metal ions (#SUKRITI GUPTA#)
6. Re: Lennard jones parameters for ions (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Fri, 25 Jul 2014 07:35:59 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Groups in index.ndx
Message-ID: <53D2411F.1080509 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 7/25/14, 7:23 AM, INPE (Ingrid Viveka Pettersson) wrote:
> Dear Group,
>
> I have defined different specific groups in the index.ndx file. My problem is that if I try to add a new group, the old ones are disappearing. Should it be like this?
>
Depends on the way you're issuing make_ndx. You can preserve the existing
custom groups when writing a new index file by supplying the old index file as
input to make_ndx. If you're using default file names (hint: always provide
your exact command!) then it will otherwise be overwritten.
make_ndx -f conf.gro -n old_index.ndx -o new_index.ndx
will preserve your custom groups and allow you to add new ones.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 2
Date: Fri, 25 Jul 2014 07:37:19 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Angle group
Message-ID: <53D2416F.5010904 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 7/25/14, 7:35 AM, Cyrus Djahedi wrote:
> There is something else. I also tried using mk_angndx to generate an index file prior to using g_angle by: "mk_angndx -s C0.tpr -type angle"
> It generates a lot of different angle group that I can not identify. Each line in the index-file has 9 atoms in it, are the atoms divided three-by-three to form a triplet? Is there any way of knowing which group represents which triplet?
>
> g_angle:
>
> Group 0 (Theta=110.0_502.42) has 7680 elements
> Group 1 (Theta=111.0_376.81) has 10560 elements
> Group 2 (Theta=112.0_837.36) has 960 elements
> Group 3 (Theta=107.5_586.15) has 4944 elements
> Group 4 (Theta=108.5_586.15) has 5616 elements
> Group 5 (Theta=109.5_460.55) has 2976 elements
> Group 6 (Theta=113.5_376.81) has 3840 elements
> Group 7 (Theta=111.6_418.68) has 1872 elements
> Group 8 (Theta=109.5_376.81) has 960 elements
> Select a group: 2
> Selected 2: 'Theta=112.0_837.36'
> Last frame 10000 time 10000.000
> Found points in the range from 93 to 124 (max 180)
> < angle > = 108.363
> < angle^2 > = 11742.5
> Std. Dev. = 0.214073
>
mk_angndx divides the groups based on their parameters, not necessarily by the
same chemical definition (i.e. the same bonded parameters may apply to different
groups in your structure). You can always identify what the groups contain by
opening the .ndx file in a text editor; all an .ndx file has is a list of atom
numbers, so it's easy to tell what is what.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 3
Date: Fri, 25 Jul 2014 13:43:05 +0200
From: Tamas Karpati <tkarpati at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] hints for core/shell optimization?
Message-ID:
<CAN5Ox5PFvNk-L8-_BLr7MYQXjJE1__CQjEb2qnBLwmsdA5_b+g at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear all,
I have two questions about geometry optimization of a crystal
with polarization via the core/shell model. I'm creating *.gro and
*.top files "by hand" and compile them with *.mdp to *.tpr via
GROMPP. My FF is also made by hand (simply because i need
to learn GROMACS). I have learnt on this list that with Buckingham
potentials I need to use the group rather than the Verlet scheme.
(1/2) Letting some of all atoms be polarizable through applying
shell particles made MDRUN segfault like this:
# ...
# Reading file AAA_opt.tpr, VERSION 4.6.3 (single precision)
# Using 2 MPI threads
#
# Steepest Descents:
# Tolerance (Fmax) = 1.00000e+01
# Number of steps = 10
# Segmentation fault1.0e-02 nm, Epot= -nan Fmax= 3.76506e+03,
atom= 1357
I imagined some divison by zero situation not handled and have put
some "random noise" on the shell particles' position so they do not
anymore start exactly at the atomic sites (meaning nonzero distances).
Seemed to work, at least no further crashes. Only energies and forces
seem very high:
# Steepest Descents:
# Tolerance (Fmax) = 1.00000e+01
# Number of steps = 10
# Step= 0, Dmax= 1.0e-02 nm, Epot= -1.36425e+07 Fmax= 2.99600e+05, atom= 160
# Step= 1, Dmax= 1.0e-02 nm, Epot= -1.62080e+07 Fmax= 1.25769e+06, atom= 160
# Step= 2, Dmax= 1.2e-02 nm, Epot= -1.95965e+07 Fmax= 6.87820e+08,
atom= 2759
# Step= 3, Dmax= 1.4e-02 nm, Epot= -2.02902e+07 Fmax= 1.30719e+09, atom= 468
# Step= 8, Dmax= 1.1e-03 nm, Epot= -2.18970e+07 Fmax= 5.77722e+09,
atom= 1095
# Step= 10, Dmax= 6.5e-04 nm, Epot= -1.96952e+07 Fmax= 3.92889e+08,
atom= 1096
# Energy minimization reached the maximum numberof steps before the forces
# reached the requestedprecision Fmax < 10.
My question is the following.
Is it (randomized shell positions) a correct procedure with GROMACS?
(2/2) Changing from a randomized x/y/z set to a fixed distance at
a random direction for the shell particles led to another unexpected result.
I scanned a range between 1e-4 to 0.1 nm and noticed that
the final core-to-shell distance is a function of the starting one.
I used niter = 10000 (note: the default is 20) as i noticed in an MD
type of job that 20, 100 or 1000 steps were insufficient for the shells
to relax within default tolerance. The cell size was ca. 3x3x3 nm.
My question is the following.
What would be the appropriate core-to-shell distance to apply?
I appreciate any help so thanks in advance.
With regards,
toma
------------------------------
Message: 4
Date: Fri, 25 Jul 2014 11:39:59 +0000
From: #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Lennard jones parameters for ions
Message-ID: <1406288402620.79588 at e.ntu.edu.sg>
Content-Type: text/plain; charset="iso-8859-1"
Dear Gromacs users,
I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential parameters already defined in OPLSAA forcefield, so I wanted to know if I want to add FE+3 in my simulation, then the LJ parameters for it will be different from that of Fe+2 or same?
I thought it will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3.
Regards
Sukriti
[https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif]
Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
------------------------------
Message: 5
Date: Fri, 25 Jul 2014 11:42:33 +0000
From: #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] Lennard jones parameters for metal ions
Message-ID: <1406288557018.58990 at e.ntu.edu.sg>
Content-Type: text/plain; charset="iso-8859-1"
Dear Gromacs users,
I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential parameters already defined in OPLSAA forcefield, so I wanted to know if I want to add FE+3 in my simulation, then the LJ parameters for it will be different from that of Fe+2 or same?
I thought it will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3.
Regards
Sukriti
[https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif]
Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI at N) | Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html>
------------------------------
Message: 6
Date: Fri, 25 Jul 2014 07:46:58 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Lennard jones parameters for ions
Message-ID: <53D243B2.6070403 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 7/25/14, 7:39 AM, #SUKRITI GUPTA# wrote:
> Dear Gromacs users,
>
>
> I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential parameters already defined in OPLSAA forcefield, so I wanted to know if I want to add FE+3 in my simulation, then the LJ parameters for it will be different from that of Fe+2 or same?
>
>
> I thought it will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3.
>
In any force field, LJ and electrostatic terms are parametrized to balance in
some way that produces some physically sensible behavior. Given the extremely
high charge density of Fe2+ and Fe3+, I see no reason to think that the LJ
parameters for one would be the same as for the other.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
--
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