[gmx-users] Re: genion

[Ewaru]

Hi Justin,

Yup, the grompp works fine. :) Gotta figure out on the Blowing Up now. (>.<)

Thank you once again!

Take care.



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Re: [gmx-users] Re: genion

[Justin Lemkul]

On 5/3/13 11:52 AM, Ewaru wrote:

Hi Justin,

Thank you for your prompt reply! My grompp goes like this: "grompp -f
minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr"

Is it in the topol.top file? The reason I'm asking this is because I
obtained this error while running MD:



Yes, you should see 12 ions and 12 fewer water molecules than you had before 
running genion.  If grompp doesn't complain, then your system is neutral.  It's 
a rather simple check.



"Fatal error:
2 particles communicated to PME node 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors";

and thus I was checking if my ions are neutralised or not.



There are a whole host of reasons this could be happening.  Neutralization is 
not a likely one.


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: genion

[Ewaru]

Hi Justin,

Thank you for your prompt reply! My grompp goes like this: "grompp -f
minim.mdp -c m4_solv_ions.gro -p topol.top -o em.tpr"

Is it in the topol.top file? The reason I'm asking this is because I
obtained this error while running MD: 

"Fatal error:
2 particles communicated to PME node 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors";

and thus I was checking if my ions are neutralised or not. 

Thanking you in advance.

Best regards




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Re: [gmx-users] Re: Genion cannot read from input

[Warren Gallin]

The problem is that genion is expecting input from the command line, telling it 
which molecules to replace with ions - usually SOL.

If you are running a script you have to script an input line for genion.

Warren Gallin

On 2013-04-27, at 2:56 PM, Nathan Bullock  wrote:

> The useful part of the error file
> 
> 
>  -f em.mdp  Inputgrompp input file with MD parameters
> -po  mdout.mdp  Output   grompp input file with MD parameters
>  -c filled_box.pdb  InputStructure file: gro g96 pdb tpr etc.
>  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
> -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>  -n  index.ndx  Input, Opt.  Index file
>  -p protein_mod_filled5.top  InputTopology file
> -pp  processed.top  Output, Opt. Topology file
>  -o   ions.tpr  Output   Run input file: tpr tpb tpa
>  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>  -e   ener.edr  Input, Opt.  Energy file
> Ignoring obsolete mdp entry 'title'
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
> Generated 2415 of the 2415 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2415 of the 2415 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> Excluding 3 bonded neighbours molecule type 'AZI'
> Excluding 1 bonded neighbours molecule type 'ZN'
> Excluding 2 bonded neighbours molecule type 'SOL'
> 
> NOTE 1 [file protein_mod_filled5.top, line 38757]:
>  System has non-zero total charge: 0.98
>  Total charge should normally be an integer. See
>  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>  for discussion on how close it should be to an integer.
> 
> Number of degrees of freedom in T-Coupling group rest is 105621.00
> Estimate for the relative computational load of the PME mesh part: 0.27
> 
> There was 1 note
> 
> Back Off! I just backed up ions.tpr to ./#ions.tpr.6#
> /usr/local/gromacs-4.5.5/bin/genion  (-:
> 
> Option Filename  Type Description
> 
>  -s   ions.tpr  InputRun input file: tpr tpb tpa
> -tabletable.xvg  Input, Opt.  xvgr/xmgr file
>  -n  index.ndx  Input, Opt.  Index file
>  -o  solv_ions.pdb  Output   Structure file: gro g96 pdb etc.
>  -g genion.log  Output   Log file
> -potpot.pdb  Output, Opt. Protein data bank file
>  -p protein_mod_filled5.top  In/Out, Opt! Topology file
> 
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -[no]version bool   no  Print version info and quit
> -niceint19  Set the nicelevel
> -xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -np  int0   Number of positive ions
> -pname   string NA  Name of the positive ion
> -pq  int1   Charge of the positive ion
> -nn  int2   Number of negative ions
> -nname   string CL  Name of the negative ion
> -nq  int-1  Charge of the negative ion
> -rminreal   0.6 Minimum distance between ions
> -[no]random  bool   yes Use random placement of ions instead of based on
>potential. The rmin option should still work
> -seedint1993Seed for random number generator
> -scale   real   0.001   Scaling factor for the potential for -pot
> -concreal   0   Specify salt concentration (mol/liter). This
> will
>add sufficient ions to reach up to the specified
>concentration as computed from the volume of the
>cell in the input .tpr file. Overrides the -np
>and -nn options.
> -[no]neutral bool   no  This option will add enough ions to neutralize
>the system. In combination with the
> concentration
>option a neutral system at a given salt
>concentration will be generated.
> 
> 
> Back Off! I just backed up genion.log to ./#genion.log.6#
> Reading file ions.tpr, VERSION 4.5.5 (single precision)
> Using a coulomb cut-off of 1 nm
> Group 0 ( System) has 50774 elements
> Group 1 (Protein) has  4072 elements
> Group 2 (  Protein-H) has  2059 elements
> Group 3 (C-alpha) has   258 elements
> Group 4 (   Backbone) has   774 elements
> Group 5 (  MainChain) has  1033 elements
> Group 6 (   MainChain+Cb) has  1269 elements
> Group 7 (MainChain+H) has  1276 elements
> Group 8 (  SideChain) has  2796 elements
> Group 9 (SideChain-H) has  1026 elements
> Group10 (Prot-Masses) has  4072 elements
> Group  

Re: [gmx-users] Re: Genion cannot read from input

[Mark Abraham]

On Sat, Apr 27, 2013 at 10:25 PM, Nathan Bullock  wrote:

> I created a text file called choices with the number corresponding to the
> ions group. I then had the text file as an argument for the genion
> function.
>

That cannot work. Read the link Justin provided.

Mark


> I still got the same input error.
>
>
>
> -
> Graduate Student
> University of Iowa
> Cheatum Research Group
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[gmx-users] Re: Genion cannot read from input

[Nathan Bullock]

The useful part of the error file


  -f em.mdp  Inputgrompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c filled_box.pdb  InputStructure file: gro g96 pdb tpr etc.
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n  index.ndx  Input, Opt.  Index file
  -p protein_mod_filled5.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o   ions.tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file
Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
Generated 2415 of the 2415 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2415 of the 2415 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'AZI'
Excluding 1 bonded neighbours molecule type 'ZN'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file protein_mod_filled5.top, line 38757]:
  System has non-zero total charge: 0.98
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
 
Number of degrees of freedom in T-Coupling group rest is 105621.00
Estimate for the relative computational load of the PME mesh part: 0.27

There was 1 note

Back Off! I just backed up ions.tpr to ./#ions.tpr.6#
/usr/local/gromacs-4.5.5/bin/genion  (-:

Option Filename  Type Description

  -s   ions.tpr  InputRun input file: tpr tpb tpa
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
  -n  index.ndx  Input, Opt.  Index file
  -o  solv_ions.pdb  Output   Structure file: gro g96 pdb etc.
  -g genion.log  Output   Log file
-potpot.pdb  Output, Opt. Protein data bank file
  -p protein_mod_filled5.top  In/Out, Opt! Topology file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-np  int0   Number of positive ions
-pname   string NA  Name of the positive ion
-pq  int1   Charge of the positive ion
-nn  int2   Number of negative ions
-nname   string CL  Name of the negative ion
-nq  int-1  Charge of the negative ion
-rminreal   0.6 Minimum distance between ions
-[no]random  bool   yes Use random placement of ions instead of based on
potential. The rmin option should still work
-seedint1993Seed for random number generator
-scale   real   0.001   Scaling factor for the potential for -pot
-concreal   0   Specify salt concentration (mol/liter). This
will
add sufficient ions to reach up to the specified
concentration as computed from the volume of the
cell in the input .tpr file. Overrides the -np
and -nn options.
-[no]neutral bool   no  This option will add enough ions to neutralize
the system. In combination with the
concentration
option a neutral system at a given salt
concentration will be generated.


Back Off! I just backed up genion.log to ./#genion.log.6#
Reading file ions.tpr, VERSION 4.5.5 (single precision)
Using a coulomb cut-off of 1 nm
Group 0 ( System) has 50774 elements
Group 1 (Protein) has  4072 elements
Group 2 (  Protein-H) has  2059 elements
Group 3 (C-alpha) has   258 elements
Group 4 (   Backbone) has   774 elements
Group 5 (  MainChain) has  1033 elements
Group 6 (   MainChain+Cb) has  1269 elements
Group 7 (MainChain+H) has  1276 elements
Group 8 (  SideChain) has  2796 elements
Group 9 (SideChain-H) has  1026 elements
Group10 (Prot-Masses) has  4072 elements
Group11 (non-Protein) has 46702 elements
Group12 (  Other) has 3 elements
Group13 (AZI) has 3 elements
Group14 ( ZN) has 1 elements
Group15 (Ion) has 1 elements
Group16 (AZI) has 3 elements
Group17 ( ZN) has 1 elements
Group18 (  Water) has 46698 elements
Group19 (SOL) has 46698 elements

[gmx-users] Re: Genion cannot read from input

[Nathan Bullock]

I created a text file called choices with the number corresponding to the
ions group. I then had the text file as an argument for the genion function.
I still got the same input error.



-
Graduate Student
University of Iowa 
Cheatum Research Group
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Re: [gmx-users] Re: Genion cannot read from input

[Justin Lemkul]

On 4/27/13 2:52 PM, Nathan Bullock wrote:

So I need to provide a group for the function genion, in the example you
provided g-energy has several group names. Where do I find the group names
for genion?



Group selection is the same for every Gromacs program.  Select by name or 
number.  Run genion interactively once and you will see exactly what you need to 
do.  The g_energy example is less relevant than the g_rms example on the same page.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: Genion cannot read from input

[Nathan Bullock]

So I need to provide a group for the function genion, in the example you
provided g-energy has several group names. Where do I find the group names
for genion?




-
Graduate Student
University of Iowa 
Cheatum Research Group
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[gmx-users] Re: genion

[Justin Lemkul]

For the fourth time in two days, I'll start with:

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing the list and ask that further comments and 
questions be posted there.


On 2/26/13 9:03 AM, Samadashvili Nino wrote:

Dear Justin,

  I am trying to add ions to my system using genion. Firstly, I define separate 
groups in my index file because I'd like Na and Cl mostly concentrated at the 
surface. However, genion does not allow me to choose the surface group (just 
the system / water groups are listed). Could you please help me with this 
problem?



It's not straightforward, but it's certainly possible.  Your index group will 
contain specific water molecules, and so those water molecules must appear as 
their own group listed in the [molecules] directive.  That requires a unique 
[moleculetype] name; even though they're just water molecules, genion must 
consider them differently.  So if you have some water molecules called "My_SOL" 
then copy spc.itp to my_spc.itp and rename the [moleculetype] as My_SOL.  Then 
in topol.top:


[ molecules ]
Protein  1
My_SOL   X
SOL  (Total water - X)

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: genion problem with divalent ions

[ran friedman]

Hi,
As a side note, you should be careful when using Mg (and probably all other
multiply charged ions, as well as large polarisable ions like I-). It's
very difficult to correctly represent the interactions of such ions in the
bulk correctly using non-polarisable force fields.
Ran

Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden

Norrgård, room 328d
http://lnu.se/ccbg



On 9 September 2012 16:10,  wrote:

>
>
> Message: 2
> Date: Sun, 9 Sep 2012 13:53:35 +0200
> From: Matthias Ernst 
> Subject: [gmx-users] genion problem with divalent ions
> To: Discussion list for GROMACS users 
> Message-ID: <504c833f.2050...@student.kit.edu>
> Content-Type: text/plain; charset="ISO-8859-15"; format=flowed
>
> Hi,
>
> I just encountered (another) strange thing with genion.
> I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp:
> 2, forcefield amber99sb), so I expected half of the system charge (-52)
> to be added as ions. BUT it added the same amount, i.e. 52 Mg ions
> instead of 26 which would be needed for neutralization. The same holds
> for Zn or Ca ions, which also are divalent in ions.itp
>
> Could it be that the routines of genion to determine the number of ions
> are not working properly? I mean, the -neutral option also does work
> only if the -conc flag is also there and provides a value > 0.0 (which
> in fact is not what I want when I just want do neutralize my system by
> adding ions...)
>
> Does anyone of you also had similar problems?
>
> Thank you,
> Matthias
>
>
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Re: [gmx-users] Re : genion

[Mark Abraham]

On 17/01/2011 8:07 PM, bharat gupta wrote:

Hi ,
My protein is having a total charge of -3.5 so in that case how many 
ions shall i add  - 3 or 4 ??


Your structure is broken, perhaps by inappropriate use of termini. Look 
at your structure in a visualization program.


Mark
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Re: [gmx-users] Re : genion

[Erik Marklund]

Hi,

How come you have half an electron in there?

Erik

bharat gupta skrev 2011-01-17 10.07:

Hi ,
My protein is having a total charge of -3.5 so in that case how many 
ions shall i add  - 3 or 4 ??

Pls help


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Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
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Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
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phone:+46 18 471 4537fax: +46 18 511 755
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[gmx-users] Re : genion

[bharat gupta]

Hi ,

My protein is having a total charge of -3.5 so in that case how many ions
shall i add  - 3 or 4 ??

Pls help



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
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Mobile no. - 010-5818-3680
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[gmx-users] Re.: genion doubt (manjula kasinathan)

[Jessé Nóbrega]

Dear manjula kasinathan


There aren't the "warning" parameter in gromacs, please remove the warning 
option in your mdp, if you need, add the flag -maxwarn in the grompp command,

grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr -maxwarn 10

your simulation presents Lincs warnings, read the gromacs's errors page:

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

good luck

Jessé



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Re: [gmx-users] Re: genion and a few other problems

[Justin A. Lemkul]

Quoting Manik Mayur :


> > Exact command lines are much more useful than your interpretation of what
> > you
> > typed.  If you just used genion -nn, that's probably insufficient
> > information.
> >
>
> Sorry for the confusion but genion won't add "Cl-" on its own unless I
> provide it with the relevant options (providing which I thought would be
> impertinent here). The only concern here was to find out "why Cl was listed
> in the [ molecules ] section of the topol.top file", hence the error as no
> such molecule was defined.
>
> But I found a workaround as to generate a .pdb file using genion, and then
> use pdb2gmx to generate .gro and topol.top files, which I see automatically
> generates a .itp file corresponding to "Cl-" and #includes it in topol.top
> apart from adding it into [ molecules ] section. So now its working but the
> question no. 3 is still on :)
>

I guess that works, but it's incredibly convoluted.  If you provide genion a
complete command line, then it should work fine, i.e.:

genion -s input.tpr -p topol.top -nn 5 -nname CL- -random

The above should be sufficient to insert 5 Cl- ions into your system, and update
your topology accordingly.



> Again sorry for the confusion(and I know its not magic :)) but "apart" from
> providing the ion name to be added etc., according to the manual, you can
> add ions by following ways-
> 1) provide no. of ions to be added by -nn.
> 2) use -neutral so that if the system already has a net charge, that will be
> compensated.
> 3) use -conc.

To get (2) and (3) to work, simply specify -pname and -nname; if this is unclear
in the manual perhaps some additional information would be useful, but truly you
should probably always default to specifying these options yourself; the
defaults are for ffgmx, which is deprecated.  If you specify -pname and -nname,
then genion will always work properly for the above command flags.



>
> > I can't comment on this specifically, but have you tried it?  Does it give
> > some
> > sort of error message if you do?
>
>
> I tried using above but grompp says its not possible. Meanwhile, I read in a
> paper(JCP2003(118),4692-4701) that they used a modified PME with 3 times
> bigger box dimension in the z-direction than the slab geometry. And I am
> using it with periodicity=xyz turned on.
>
> So unless I use walls, I can't use periodicity=xy with coulumb-type=PME and
> ewald_geom=3dc, Is that right?
>

Seems like that should be right; what is the exact error message that grompp is
giving you?  That is more informative than saying "its not possible."

-Justin



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalem...@vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] Re: genion and a few other problems

[Manik Mayur]

On Sat, Dec 27, 2008 at 6:36 PM, Justin A. Lemkul  wrote:

> Quoting Manik Mayur :
>
> > On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur 
> wrote:
> >
> > > Hi all,
> > >
> > > I have a few probIems/confusions and will be extremely thankful for any
> > > help. I added some "Cl- ions" by replacing water using "genion (and
> -nn)".
> > > It generated a "topol.top" file with Cl listed in [ molecules ]. Now
> when I
> > > try to run grompp, it gives an error saying "no such molecule type Cl".
> So
> > > my questions are:
>
> Exact command lines are much more useful than your interpretation of what
> you
> typed.  If you just used genion -nn, that's probably insufficient
> information.
>

Sorry for the confusion but genion won't add "Cl-" on its own unless I
provide it with the relevant options (providing which I thought would be
impertinent here). The only concern here was to find out "why Cl was listed
in the [ molecules ] section of the topol.top file", hence the error as no
such molecule was defined.

But I found a workaround as to generate a .pdb file using genion, and then
use pdb2gmx to generate .gro and topol.top files, which I see automatically
generates a .itp file corresponding to "Cl-" and #includes it in topol.top
apart from adding it into [ molecules ] section. So now its working but the
question no. 3 is still on :)

> > 1) How to avoid that error? Do I have to define a Cl.itp and add
> molecule
> > > type etc. ?
>
> Check ions.itp for the proper ion nomenclature for whatever force field
> you're
> using.  Different force fields use different naming.


ok


>
>
> > > 2) If I try to add Cl using -neutral option (as my system before
> already
> > > had a net +ve charge), it says "No ions to add and no potentials to
> > > calculate", why?
>
> Probably because your command line was just genion -neutral, right?  You
> didn't
> tell genion what type of ions to add, so it's not going to do anything;
> it's
> not magic!
>

Again sorry for the confusion(and I know its not magic :)) but "apart" from
providing the ion name to be added etc., according to the manual, you can
add ions by following ways-
1) provide no. of ions to be added by -nn.
2) use -neutral so that if the system already has a net charge, that will be
compensated.
3) use -conc.
The first one works, but the second one is giving the above mentioned error.

> > 3) Why is Cl listed in molecules and not [atoms] section?
>
> If you properly #include "ions.itp" then it is an additional moleculetype
> definition within the topology.
>
> > > 4) If I wish to use SPC/E model, do I have to use ffgmx*. I tried using
> > > ffG43a1* with #include "spce.itp" in topol.top. Is that correct? what
> else
> > I
>
> You should not use ffgmx for anything.  Using #include "spce.itp" is
> correct for
> use with other force fields.
>

ok

> > would have to do?
> > > 5) Is it mandatory to have periodicity=xyz with coulumb-type=PME and
> ewald
> > > geom=3dc, other than using walls option(I have my own channel walls in
> the
> > > system, so want to avoid them). Is there a way to use periodicity=xyz
> with
> > > coulumb-type=PME and ewald geom=3dc?
> > >
> > Is there a way to use periodicity=xy with coulumb-type=PME and ewald
> > geom=3dc?
> > >
>
> I can't comment on this specifically, but have you tried it?  Does it give
> some
> sort of error message if you do?


I tried using above but grompp says its not possible. Meanwhile, I read in a
paper(JCP2003(118),4692-4701) that they used a modified PME with 3 times
bigger box dimension in the z-direction than the slab geometry. And I am
using it with periodicity=xyz turned on.

So unless I use walls, I can't use periodicity=xy with coulumb-type=PME and
ewald_geom=3dc, Is that right?

-Justin
>

Thanks,
Manik

> > Thanks,
> > > Manik
> > >
> > > --
> > > _
> > > HAPAX LEGOMENA
> > >
> >
> >
> >
> > --
> > _
> > HAPAX LEGOMENA
> >
>
>
>
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalem...@vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> 
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-- 
_
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Re: [gmx-users] Re: genion and a few other problems

[Justin A. Lemkul]

Quoting Manik Mayur :

> On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur  wrote:
>
> > Hi all,
> >
> > I have a few probIems/confusions and will be extremely thankful for any
> > help. I added some "Cl- ions" by replacing water using "genion (and -nn)".
> > It generated a "topol.top" file with Cl listed in [ molecules ]. Now when I
> > try to run grompp, it gives an error saying "no such molecule type Cl". So
> > my questions are:

Exact command lines are much more useful than your interpretation of what you
typed.  If you just used genion -nn, that's probably insufficient information.

> > 1) How to avoid that error? Do I have to define a Cl.itp and add molecule
> > type etc. ?

Check ions.itp for the proper ion nomenclature for whatever force field you're
using.  Different force fields use different naming.

> > 2) If I try to add Cl using -neutral option (as my system before already
> > had a net +ve charge), it says "No ions to add and no potentials to
> > calculate", why?

Probably because your command line was just genion -neutral, right?  You didn't
tell genion what type of ions to add, so it's not going to do anything; it's
not magic!

> > 3) Why is Cl listed in molecules and not [atoms] section?

If you properly #include "ions.itp" then it is an additional moleculetype
definition within the topology.

> > 4) If I wish to use SPC/E model, do I have to use ffgmx*. I tried using
> > ffG43a1* with #include "spce.itp" in topol.top. Is that correct? what else
> I

You should not use ffgmx for anything.  Using #include "spce.itp" is correct for
use with other force fields.

> > would have to do?
> > 5) Is it mandatory to have periodicity=xyz with coulumb-type=PME and ewald
> > geom=3dc, other than using walls option(I have my own channel walls in the
> > system, so want to avoid them). Is there a way to use periodicity=xyz with
> > coulumb-type=PME and ewald geom=3dc?
> >
> Is there a way to use periodicity=xy with coulumb-type=PME and ewald
> geom=3dc?
> >

I can't comment on this specifically, but have you tried it?  Does it give some
sort of error message if you do?

-Justin

> > Thanks,
> > Manik
> >
> > --
> > _
> > HAPAX LEGOMENA
> >
>
>
>
> --
> _
> HAPAX LEGOMENA
>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalem...@vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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[gmx-users] Re: genion and a few other problems

[Manik Mayur]

On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur  wrote:

> Hi all,
>
> I have a few probIems/confusions and will be extremely thankful for any
> help. I added some "Cl- ions" by replacing water using "genion (and -nn)".
> It generated a "topol.top" file with Cl listed in [ molecules ]. Now when I
> try to run grompp, it gives an error saying "no such molecule type Cl". So
> my questions are:
> 1) How to avoid that error? Do I have to define a Cl.itp and add molecule
> type etc. ?
> 2) If I try to add Cl using -neutral option (as my system before already
> had a net +ve charge), it says "No ions to add and no potentials to
> calculate", why?
> 3) Why is Cl listed in molecules and not [atoms] section?
> 4) If I wish to use SPC/E model, do I have to use ffgmx*. I tried using
> ffG43a1* with #include "spce.itp" in topol.top. Is that correct? what else I
> would have to do?
> 5) Is it mandatory to have periodicity=xyz with coulumb-type=PME and ewald
> geom=3dc, other than using walls option(I have my own channel walls in the
> system, so want to avoid them). Is there a way to use periodicity=xyz with
> coulumb-type=PME and ewald geom=3dc?
>
Is there a way to use periodicity=xy with coulumb-type=PME and ewald
geom=3dc?
>
> Thanks,
> Manik
>
> --
> _
> HAPAX LEGOMENA
>



-- 
_
HAPAX LEGOMENA
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Re: [gmx-users] Re: genion causing atom to be in multiple T-Coupling groups

[Tsjerk Wassenaar]

Una,

In your case you can also try the T-coupling groups Protein and
Non-Protein, without providing a .ndx file. However, in general give
some thoughts to temperature coupling (groups) when setting up your
system and try to grasp how groups are treated in gromacs.

Hope it helps,

Tsjerk

On 9/11/06, David van der Spoel <[EMAIL PROTECTED]> wrote:

Una Bjarnadottir wrote:
> Una Bjarnadottir wrote:
>
>>> Dear Users,
>>>
>>> I'm hoping for an answear on my problem with neutralizing my system
>>> adding 3 Cl ions with genion.  When running grompp after genion with
>>> the new generated .gro file I get this error:
>>>
>>> Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)
>>>
>>> which is the last water atom (total in system 33003) and groups 15
>>> and 1 are Cl and protein groups if I on the other hand do not
>>> neutralize the system the run goes fine!  When looking into the .ndx
>>> file atom 33000 is in 4 groups;  0 (system), 11 (non-protein), 14
>>> (SOL) and 16 (other).  How can I change the group definitions and
>>> make sure the groups do not overlap and to be unique?
>>> It seems to be something wrong with how the genion works for me.  I
>>> followed the tutorial and chose the SOL group and water molecules
>>> were replaced by the Cl ions.  Than I modifyed the .top file and took
>>> 3 sol molecules and added the 3 ions.
>>>
>>> Please help because have not been able to fix the problem with
>>> related letters on the subject on the list.
>>>
>>> Best regards, Una Bjarnadottir
>>>
>>
>>
>>> What do your tcoupl groups look like?
>
> tc-grps':'Protein OTHER CL-  ###where I have to call SOL: OTHER
> otherwise error
>
>>> Could it be System SOL?
>
>>> The number may be confusing, you should subtract one from them when
>>> compared to the output from gmxcheck -n index.ndx
>>> So it seems that atom 33000 (numbering in the coordinate file) is in
>>> groups 14 and 0. Maybe you should make a new index file after genion.
>>> Note that it is good practice to make the ions part of the solvent T
>>> coupling group.
>
> I made the indes file after running genion using the .gro output file
> from genion generating it.  Also I thought you would have to subtract
> one and it was groups 14 and 0 instead of 15 and 1.  How would I have
> the ions part of the solvent T coupling group?  By modifying the .top
> file to [ molecules ]
> ; Compound#mols
> Protein_E   1
> Protein_I   1
> Protein_A   1
> SOL+CL-  9719
>
> and than the tc-grps in the .mdp file accordingly to that.  How will I
> define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal
> error: No such moleculetype SOL+CL- came for both.
> Best regards David for your reply, Una David.

in make_ndx you type
14 | 15
that will give you the combination of the two groups (if 14 is SOL and
15 is CL-)

>
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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se

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--
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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Re: [gmx-users] Re: genion causing atom to be in multiple T-Coupling groups

[David van der Spoel]

Una Bjarnadottir wrote:

Una Bjarnadottir wrote:


Dear Users,

I'm hoping for an answear on my problem with neutralizing my system 
adding 3 Cl ions with genion.  When running grompp after genion with 
the new generated .gro file I get this error:


Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 
and 1 are Cl and protein groups if I on the other hand do not 
neutralize the system the run goes fine!  When looking into the .ndx 
file atom 33000 is in 4 groups;  0 (system), 11 (non-protein), 14 
(SOL) and 16 (other).  How can I change the group definitions and 
make sure the groups do not overlap and to be unique?
It seems to be something wrong with how the genion works for me.  I 
followed the tutorial and chose the SOL group and water molecules 
were replaced by the Cl ions.  Than I modifyed the .top file and took 
3 sol molecules and added the 3 ions.


Please help because have not been able to fix the problem with 
related letters on the subject on the list.


Best regards, Una Bjarnadottir

 


What do your tcoupl groups look like?


tc-grps':'Protein OTHER CL-  ###where I have to call SOL: OTHER 
otherwise error



Could it be System SOL?


The number may be confusing, you should subtract one from them when 
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in 
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T 
coupling group.


I made the indes file after running genion using the .gro output file 
from genion generating it.  Also I thought you would have to subtract 
one and it was groups 14 and 0 instead of 15 and 1.  How would I have 
the ions part of the solvent T coupling group?  By modifying the .top 
file to [ molecules ]

; Compound#mols
Protein_E   1
Protein_I   1
Protein_A   1
SOL+CL-  9719

and than the tc-grps in the .mdp file accordingly to that.  How will I 
define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal 
error: No such moleculetype SOL+CL- came for both.

Best regards David for your reply, Una David.


in make_ndx you type
14 | 15
that will give you the combination of the two groups (if 14 is SOL and 
15 is CL-)




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Re: genion causing atom to be in multiple T-Coupling groups

[Una Bjarnadottir]

Una Bjarnadottir wrote:


Dear Users,

I'm hoping for an answear on my problem with neutralizing my system 
adding 3 Cl ions with genion.  When running grompp after genion with the 
new generated .gro file I get this error:


Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

which is the last water atom (total in system 33003) and groups 15 and 1 
are Cl and protein groups if I on the other hand do not neutralize the 
system the run goes fine!  When looking into the .ndx file atom 33000 is 
in 4 groups;  0 (system), 11 (non-protein), 14 (SOL) and 16 (other).  
How can I change the group definitions and make sure the groups do not 
overlap and to be unique?
It seems to be something wrong with how the genion works for me.  I 
followed the tutorial and chose the SOL group and water molecules were 
replaced by the Cl ions.  Than I modifyed the .top file and took 3 sol 
molecules and added the 3 ions.


Please help because have not been able to fix the problem with related 
letters on the subject on the list.


Best regards, Una Bjarnadottir

 


What do your tcoupl groups look like?


tc-grps':'Protein OTHER CL-  ###where I have to call SOL: OTHER otherwise error


Could it be System SOL?


The number may be confusing, you should subtract one from them when 
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in 
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T 
coupling group.


I made the indes file after running genion using the .gro output file from genion generating it.  Also I thought you would have to subtract one and it was groups 14 and 0 instead of 15 and 1.  How would I have the ions part of the solvent T coupling group?  By modifying the .top file to 
[ molecules ]

; Compound#mols
Protein_E   1
Protein_I   1
Protein_A   1
SOL+CL-  9719

and than the tc-grps in the .mdp file accordingly to that.  How will I define SOL and CL- together, I tryed 
SOL+CL- and SOL-CL- but Fatal error: No such moleculetype SOL+CL- came for both. 

Best regards David for your reply, Una 
David.


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