Re: [gmx-users] genion without stdin

[Justin Lemkul]

On 2/13/20 5:59 AM, Christian Blau wrote:

Hello Matthias,


yes, if you use an indexfile with exactly one index group inside, this 
index group will be automatically picked.



(like

[ solvent ]

1001 1002 1003 1004 1005 1006 1007 1008 1009  ...

and nothing else



It's even easier than that:

echo "SOL" | gmx genion ...

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] genion without stdin

[Christian Blau]

Hello Matthias,


yes, if you use an indexfile with exactly one index group inside, this index 
group will be automatically picked.


(like

[ solvent ]

1001 1002 1003 1004 1005 1006 1007 1008 1009  ...

and nothing else


Best,

Christian


On 2020-02-13 11:49, Urban, Matthias wrote:

Hello mailinglist,


is there a way to prevent "gmx genion" from expecting input via stdin?


I am using gromacs v2020 with gmxapi.


Thanks in advance.


Cheers,


Matthias

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[gmx-users] genion without stdin

[Urban, Matthias]

Hello mailinglist,


is there a way to prevent "gmx genion" from expecting input via stdin?


I am using gromacs v2020 with gmxapi.


Thanks in advance.


Cheers,


Matthias
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Re: [gmx-users] genion problem with topology

[Justin Lemkul]

On 7/3/18 1:47 PM, gangotri dey wrote:

Dear all,

I have replaced one water molecule in the solvent with a Cl atom using
genion. My syntax is as follows:

gmx_mpi genion -s ions.tpr -o solvate.gro -p topol.top -pname NA -nn 1
-nname CL

I have generated the ions.tpr using the ion.mdp file as in the tutorial
from Bevan group.
I see that the topol.top adds CL at the end under [molecules] but when I
try to minimize the geometry using the new solvate.gro file the error as
given as

ERROR 1 [file topol.top, line 37]:
   No such moleculetype CL

I do not understand how I can rectify the problem. Can someone help?


The ion [moleculetype] definitions are all handled by ions.itp in the 
parent force field. Make sure you're following the force field's naming 
convention and make sure #include "whatever.ff/ions.itp" is in your .top 
file (it should if produced by pdb2gmx).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] genion problem with topology

[Shrinath Kumar]

What forcefield are you using? Check if CL is defined in your forcefield
(it's probably not, which is why you are getting the error). Each type
under [ molecules ] must have a corresponding [ moleculetype ] section
defined somewhere in your forcefield files.

On 3 July 2018 at 18:47, gangotri dey  wrote:

> Dear all,
>
> I have replaced one water molecule in the solvent with a Cl atom using
> genion. My syntax is as follows:
>
> gmx_mpi genion -s ions.tpr -o solvate.gro -p topol.top -pname NA -nn 1
> -nname CL
>
> I have generated the ions.tpr using the ion.mdp file as in the tutorial
> from Bevan group.
> I see that the topol.top adds CL at the end under [molecules] but when I
> try to minimize the geometry using the new solvate.gro file the error as
> given as
>
> ERROR 1 [file topol.top, line 37]:
>   No such moleculetype CL
>
> I do not understand how I can rectify the problem. Can someone help?
>
> *Thank you*
>
> *Gangotri Dey*
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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[gmx-users] genion problem with topology

[gangotri dey]

Dear all,

I have replaced one water molecule in the solvent with a Cl atom using
genion. My syntax is as follows:

gmx_mpi genion -s ions.tpr -o solvate.gro -p topol.top -pname NA -nn 1
-nname CL

I have generated the ions.tpr using the ion.mdp file as in the tutorial
from Bevan group.
I see that the topol.top adds CL at the end under [molecules] but when I
try to minimize the geometry using the new solvate.gro file the error as
given as

ERROR 1 [file topol.top, line 37]:
  No such moleculetype CL

I do not understand how I can rectify the problem. Can someone help?

*Thank you*

*Gangotri Dey*
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Re: [gmx-users] Genion

[Sergio Manzetti]

Indeed. Thanks! 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Mark Abraham" <mark.j.abra...@gmail.com> 
To: "gmx-users" <gmx-us...@gromacs.org> 
Sent: Thursday, June 22, 2017 2:29:54 PM 
Subject: Re: [gmx-users] Genion 

Hi, 

The error message has a helpful URL that'll take you to the same advice 
that we give several times a week on here :-) 

Mark 

On Thu, 22 Jun 2017 14:27 Sergio Manzetti <sergio.manze...@fjordforsk.no> 
wrote: 

> Thanks, Worked out. Now I got a note saying: 
> 
> NOTE 1 [file em.mdp]: 
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be 
> removed in a future release when all interaction forms are supported for 
> the verlet scheme. The verlet scheme already scales better, and it is 
> compatible with GPUs and other accelerators. 
> 
> 
> 
> Fatal error: 
> 1 particles communicated to PME rank 3 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 
> 
> 
> 
> How can I fix the system, when the energy minimization step cannot? 
> 
> 
> Sergio 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
> | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ 
> http://www.phap.no/ | FAP ] 
> 
> 
> 
> From: "Justin Lemkul" <jalem...@vt.edu> 
> To: "gmx-users" <gmx-us...@gromacs.org> 
> Sent: Thursday, June 22, 2017 2:21:17 PM 
> Subject: Re: [gmx-users] Genion 
> 
> On 6/22/17 8:14 AM, Sergio Manzetti wrote: 
> > OK, now I treied writing Na Cl and not NA and CL and get: 
> > 
> 
> This is what you did before, so naturally you get the same thing. 
> 
> > Na) 
> > Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > 
> 
> As I said, using mixed case is incorrect. The [moleculetype] entries in 
> ions.itp expect all caps. Use all caps. 
> 
> -Justin 
> 
> > 
> > 
> > 
> > 
> > Sergio Manzetti 
> > 
> > [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> > 
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ 
> http://www.fjordforsk.no/ | ] 
> > Midtun 
> > 6894 Vangsnes 
> > Norge 
> > Org.nr. 911 659 654 
> > Tlf: +47 57695621 
> > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ 
> | FAP ] 
> > 
> > 
> > 
> > From: "Justin Lemkul" <jalem...@vt.edu> 
> > To: "gmx-users" <gmx-us...@gromacs.org> 
> > Sent: Thursday, June 22, 2017 2:09:02 PM 
> > Subject: Re: [gmx-users] Genion 
> > 
> > On 6/22/17 7:30 AM, Sergio Manzetti wrote: 
> >> Hi, the procedure as defined by Juistin worked out well. However, a new 
> problem has occurred. At mdrun for the minimization, I get: 
> >> 
> >> --- 
> >> Program gmx mdrun, VERSION 5.1.2 
> >> Source code file: 
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
> line: 276 
> >> 
> >> Fatal error: 
> >> 1 particles communicated to PME rank 3 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 h

Re: [gmx-users] Genion

[Sergio Manzetti]

THanks Justin. 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul" <jalem...@vt.edu> 
To: "gmx-users" <gmx-us...@gromacs.org> 
Sent: Thursday, June 22, 2017 2:29:40 PM 
Subject: Re: [gmx-users] Genion 

On 6/22/17 8:22 AM, Sergio Manzetti wrote: 
> Thanks, Worked out. Now I got a note saying: 
> 
> NOTE 1 [file em.mdp]: 
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be 
> removed in a future release when all interaction forms are supported for 
> the verlet scheme. The verlet scheme already scales better, and it is 
> compatible with GPUs and other accelerators. 
> 
> 
> 
> Fatal error: 
> 1 particles communicated to PME rank 3 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 
> 
> 
> 
> How can I fix the system, when the energy minimization step cannot? 
> 

You haven't provided any information about the force field you're using, .mdp 
settings, etc. so there's nothing to go on. If this is an immediate failure, 
visualize your starting coordinates because there's something wrong. Otherwise, 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
 

-Justin 

-- 
== 

Justin A. Lemkul, Ph.D. 
Ruth L. Kirschstein NRSA Postdoctoral Fellow 

Department of Pharmaceutical Sciences 
School of Pharmacy 
Health Sciences Facility II, Room 629 
University of Maryland, Baltimore 
20 Penn St. 
Baltimore, MD 21201 

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul 

== 
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Re: [gmx-users] Genion

[Mark Abraham]

Hi,

The error message has a helpful URL that'll take you to the same advice
that we give several times a week on here :-)

Mark

On Thu, 22 Jun 2017 14:27 Sergio Manzetti <sergio.manze...@fjordforsk.no>
wrote:

> Thanks, Worked out. Now I got a note saying:
>
> NOTE 1 [file em.mdp]:
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be
> removed in a future release when all interaction forms are supported for
> the verlet scheme. The verlet scheme already scales better, and it is
> compatible with GPUs and other accelerators.
>
>
>
> Fatal error:
> 1 particles communicated to PME rank 3 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
>
>
>
> How can I fix the system, when the energy minimization step cannot?
>
>
> Sergio
>
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
>
>
>
> From: "Justin Lemkul" <jalem...@vt.edu>
> To: "gmx-users" <gmx-us...@gromacs.org>
> Sent: Thursday, June 22, 2017 2:21:17 PM
> Subject: Re: [gmx-users] Genion
>
> On 6/22/17 8:14 AM, Sergio Manzetti wrote:
> > OK, now I treied writing Na Cl and not NA and CL and get:
> >
>
> This is what you did before, so naturally you get the same thing.
>
> > Na)
> > Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >
>
> As I said, using mixed case is incorrect. The [moleculetype] entries in
> ions.itp expect all caps. Use all caps.
>
> -Justin
>
> >
> >
> >
> >
> > Sergio Manzetti
> >
> > [ http://www.fjordforsk.no/logo_hr2.jpg ]
> >
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [
> http://www.fjordforsk.no/ | ]
> > Midtun
> > 6894 Vangsnes
> > Norge
> > Org.nr. 911 659 654
> > Tlf: +47 57695621
> > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ |
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/
> | FAP ]
> >
> >
> >
> > From: "Justin Lemkul" <jalem...@vt.edu>
> > To: "gmx-users" <gmx-us...@gromacs.org>
> > Sent: Thursday, June 22, 2017 2:09:02 PM
> > Subject: Re: [gmx-users] Genion
> >
> > On 6/22/17 7:30 AM, Sergio Manzetti wrote:
> >> Hi, the procedure as defined by Juistin worked out well. However, a new
> problem has occurred. At mdrun for the minimization, I get:
> >>
> >> ---
> >> Program gmx mdrun, VERSION 5.1.2
> >> Source code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp,
> line: 276
> >>
> >> Fatal error:
> >> 1 particles communicated to PME rank 3 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
> >>
> >>
> >> This may be caused by the solvent replacement of genion by Na Cl:
> >>
> >>
> >>
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
> >> Will try to add 130 Na ions and 90 Cl ions.
> >> Select a continuous group of solvent molecules
> >> Group 0 ( System) has 98254 elements
> >> Group 1 ( DNA) has 1333 elements
> >> Group 2 ( Water) has 96921 elements
> >> Group 3 ( SOL) has 96921 elements
> >> Group 4 ( non-Water) has 1333 elements
&

Re: [gmx-users] Genion

[Justin Lemkul]

On 6/22/17 8:22 AM, Sergio Manzetti wrote:

Thanks, Worked out. Now I got a note saying:

NOTE 1 [file em.mdp]:
The group cutoff scheme is deprecated since GROMACS 5.0 and will be
removed in a future release when all interaction forms are supported for
the verlet scheme. The verlet scheme already scales better, and it is
compatible with GPUs and other accelerators.



Fatal error:
1 particles communicated to PME rank 3 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



How can I fix the system, when the energy minimization step cannot?



You haven't provided any information about the force field you're using, .mdp 
settings, etc. so there's nothing to go on.  If this is an immediate failure, 
visualize your starting coordinates because there's something wrong. Otherwise, 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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Re: [gmx-users] Genion

[Sergio Manzetti]

Thanks, Worked out. Now I got a note saying: 

NOTE 1 [file em.mdp]: 
The group cutoff scheme is deprecated since GROMACS 5.0 and will be 
removed in a future release when all interaction forms are supported for 
the verlet scheme. The verlet scheme already scales better, and it is 
compatible with GPUs and other accelerators. 



Fatal error: 
1 particles communicated to PME rank 3 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 



How can I fix the system, when the energy minimization step cannot? 


Sergio 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul" <jalem...@vt.edu> 
To: "gmx-users" <gmx-us...@gromacs.org> 
Sent: Thursday, June 22, 2017 2:21:17 PM 
Subject: Re: [gmx-users] Genion 

On 6/22/17 8:14 AM, Sergio Manzetti wrote: 
> OK, now I treied writing Na Cl and not NA and CL and get: 
> 

This is what you did before, so naturally you get the same thing. 

> Na) 
> Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> 

As I said, using mixed case is incorrect. The [moleculetype] entries in 
ions.itp expect all caps. Use all caps. 

-Justin 

> 
> 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
> FAP ] 
> 
> 
> 
> From: "Justin Lemkul" <jalem...@vt.edu> 
> To: "gmx-users" <gmx-us...@gromacs.org> 
> Sent: Thursday, June 22, 2017 2:09:02 PM 
> Subject: Re: [gmx-users] Genion 
> 
> On 6/22/17 7:30 AM, Sergio Manzetti wrote: 
>> Hi, the procedure as defined by Juistin worked out well. However, a new 
>> problem has occurred. At mdrun for the minimization, I get: 
>> 
>> --- 
>> Program gmx mdrun, VERSION 5.1.2 
>> Source code file: 
>> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
>> line: 276 
>> 
>> Fatal error: 
>> 1 particles communicated to PME rank 3 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 
>> 
>> 
>> This may be caused by the solvent replacement of genion by Na Cl: 
>> 
>> 
>> 
>> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
>> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
>> Will try to add 130 Na ions and 90 Cl ions. 
>> Select a continuous group of solvent molecules 
>> Group 0 ( System) has 98254 elements 
>> Group 1 ( DNA) has 1333 elements 
>> Group 2 ( Water) has 96921 elements 
>> Group 3 ( SOL) has 96921 elements 
>> Group 4 ( non-Water) has 1333 elements 
>> Select a group: 3 
>> Selected 3: 'SOL' 
>> Number of (3-atomic) solvent molecules: 32307 
>> Replacing solvent molecule 3244 (atom 11065) with Na 
>> Replacing solvent molecule 8993 (atom 28312) with Na 
>> Replacing solvent molecule 7088 (atom 22597) with Na 
>> Replacing solvent molecule 29442 (atom 89659) with Na 
>> Replacing solvent molecule 30079 (atom 91570) with Na 
>> Replacing solvent molecule 5128 (atom 16717) with Na 
>> Replacing solvent molecule 10705 (atom 33448) with Na 
>> Replacing solvent molecule 1418 (atom 5587) with Na 
>> Replacing solvent molecule 6608 (atom 21157

Re: [gmx-users] Genion

[Justin Lemkul]

On 6/22/17 8:14 AM, Sergio Manzetti wrote:

OK, now I treied writing Na Cl and not NA and CL and get:



This is what you did before, so naturally you get the same thing.


Na)
Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)



As I said, using mixed case is incorrect.  The [moleculetype] entries in 
ions.itp expect all caps.  Use all caps.


-Justin






Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]



From: "Justin Lemkul" <jalem...@vt.edu>
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Thursday, June 22, 2017 2:09:02 PM
Subject: Re: [gmx-users] Genion

On 6/22/17 7:30 AM, Sergio Manzetti wrote:

Hi, the procedure as defined by Juistin worked out well. However, a new problem 
has occurred. At mdrun for the minimization, I get:

---
Program gmx mdrun, VERSION 5.1.2
Source code file: 
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
line: 276

Fatal error:
1 particles communicated to PME rank 3 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


This may be caused by the solvent replacement of genion by Na Cl:



Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
Will try to add 130 Na ions and 90 Cl ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 98254 elements
Group 1 ( DNA) has 1333 elements
Group 2 ( Water) has 96921 elements
Group 3 ( SOL) has 96921 elements
Group 4 ( non-Water) has 1333 elements
Select a group: 3
Selected 3: 'SOL'
Number of (3-atomic) solvent molecules: 32307
Replacing solvent molecule 3244 (atom 11065) with Na
Replacing solvent molecule 8993 (atom 28312) with Na
Replacing solvent molecule 7088 (atom 22597) with Na
Replacing solvent molecule 29442 (atom 89659) with Na
Replacing solvent molecule 30079 (atom 91570) with Na
Replacing solvent molecule 5128 (atom 16717) with Na
Replacing solvent molecule 10705 (atom 33448) with Na
Replacing solvent molecule 1418 (atom 5587) with Na
Replacing solvent molecule 6608 (atom 21157) with Na
Replacing solvent molecule 28124 (atom 85705) with Na
Replacing solvent molecule 5440 (atom 17653) with Na
Replacing solvent molecule 31518 (atom 95887) with Na
Replacing solvent molecule 16384 (atom 50485) with Na
Replacing solvent molecule 17675 (atom 54358) with Na
Replacing solvent molecule 23446 (atom 71671) with Na
Replacing solvent molecule 15659 (atom 48310) with Na
Replacing solvent molecule 18442 (atom 56659) with Na
Replacing solvent molecule 23777 (atom 72664) with Na
Replacing solvent molecule 5965 (atom 19228) with Na
Replacing solvent molecule 15375 (atom 47458) with Na
Replacing solvent molecule 30985 (atom 94288) with Na
Replacing solvent molecule 19076 (atom 58561) with Na
Replacing solvent molecule 18065 (atom 55528) with Na
Replacing solvent molecule 22711 (atom 69466) with Na
Replacing solvent molecule 27097 (atom 82624) with Na
Replacing solvent molecule 21561 (atom 66016) with Na
Replacing solvent molecule 18592 (atom 57109) with Na
Replacing solvent molecule 22174 (atom 67855) with Na
Replacing solvent molecule 17888 (atom 54997) with Na
Replacing solvent molecule 13005 (atom 40348) with Na
Replacing solvent molecule 3481 (atom 11776) with Na
Replacing solvent molecule 22603 (atom 69142) with Na
Replacing solvent molecule 9899 (atom 31030) with Na
Replacing solvent molecule 3438 (atom 11647) with Na
Replacing solvent molecule 12180 (atom 37873) with Na
Replacing solvent molecule 32219 (atom 97990) with Na
Replacing solvent molecule 23159 (atom 70810) with Na
Replacing solvent molecule 27929 (atom 85120) with Na


which then reflects on grompp as:



Setting the LD random seed to 3274024379
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA_chain_E'
Excluding 3 bonded neighbours molecule type 'DNA_chain_F'
Excluding 2 bonded neighbours molecu

Re: [gmx-users] Genion

[Sergio Manzetti]

OK, now I treied writing Na Cl and not NA and CL and get: 

Na) 
Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 





Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul" <jalem...@vt.edu> 
To: "gmx-users" <gmx-us...@gromacs.org> 
Sent: Thursday, June 22, 2017 2:09:02 PM 
Subject: Re: [gmx-users] Genion 

On 6/22/17 7:30 AM, Sergio Manzetti wrote: 
> Hi, the procedure as defined by Juistin worked out well. However, a new 
> problem has occurred. At mdrun for the minimization, I get: 
> 
> --- 
> Program gmx mdrun, VERSION 5.1.2 
> Source code file: 
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
> line: 276 
> 
> Fatal error: 
> 1 particles communicated to PME rank 3 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 
> 
> 
> This may be caused by the solvent replacement of genion by Na Cl: 
> 
> 
> 
> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
> Will try to add 130 Na ions and 90 Cl ions. 
> Select a continuous group of solvent molecules 
> Group 0 ( System) has 98254 elements 
> Group 1 ( DNA) has 1333 elements 
> Group 2 ( Water) has 96921 elements 
> Group 3 ( SOL) has 96921 elements 
> Group 4 ( non-Water) has 1333 elements 
> Select a group: 3 
> Selected 3: 'SOL' 
> Number of (3-atomic) solvent molecules: 32307 
> Replacing solvent molecule 3244 (atom 11065) with Na 
> Replacing solvent molecule 8993 (atom 28312) with Na 
> Replacing solvent molecule 7088 (atom 22597) with Na 
> Replacing solvent molecule 29442 (atom 89659) with Na 
> Replacing solvent molecule 30079 (atom 91570) with Na 
> Replacing solvent molecule 5128 (atom 16717) with Na 
> Replacing solvent molecule 10705 (atom 33448) with Na 
> Replacing solvent molecule 1418 (atom 5587) with Na 
> Replacing solvent molecule 6608 (atom 21157) with Na 
> Replacing solvent molecule 28124 (atom 85705) with Na 
> Replacing solvent molecule 5440 (atom 17653) with Na 
> Replacing solvent molecule 31518 (atom 95887) with Na 
> Replacing solvent molecule 16384 (atom 50485) with Na 
> Replacing solvent molecule 17675 (atom 54358) with Na 
> Replacing solvent molecule 23446 (atom 71671) with Na 
> Replacing solvent molecule 15659 (atom 48310) with Na 
> Replacing solvent molecule 18442 (atom 56659) with Na 
> Replacing solvent molecule 23777 (atom 72664) with Na 
> Replacing solvent molecule 5965 (atom 19228) with Na 
> Replacing solvent molecule 15375 (atom 47458) with Na 
> Replacing solvent molecule 30985 (atom 94288) with Na 
> Replacing solvent molecule 19076 (atom 58561) with Na 
> Replacing solvent molecule 18065 (atom 55528) with Na 
> Replacing solvent molecule 22711 (atom 69466) with Na 
> Replacing solvent molecule 27097 (atom 82624) with Na 
> Replacing solvent molecule 21561 (atom 66016) with Na 
> Replacing solvent molecule 18592 (atom 57109) with Na 
> Replacing solvent molecule 22174 (atom 67855) with Na 
> Replacing solvent molecule 17888 (atom 54997) with Na 
> Replacing solvent molecule 13005 (atom 40348) with Na 
> Replacing solvent molecule 3481 (atom 11776) with Na 
> Replacing solvent molecule 22603 (atom 69142) with Na 
> Replacing solvent molecule 9899 (atom 31030) with Na 
> Replacing solvent molecule 3438 (atom 11647) with Na 
> Replacing solvent molecule 12180 (atom 37873) with Na 
> Replacing solvent molecule 32219 (atom 97990) with Na 
> Replacing solvent molecule 23159 (atom 70810) with Na 
> Replacing solvent molecule 27929 (atom 85120) with Na 
> 
> 
> which then reflects on grompp as: 
> 
> 
> 
> Setting the LD random seed to 3274024379 
> Generated 2211 of the 2211 non-bonded parameter combinations 
>

Re: [gmx-users] Genion

[Justin Lemkul]

On 6/22/17 7:30 AM, Sergio Manzetti wrote:

Hi, the procedure as defined by Juistin worked out well. However, a new problem 
has occurred. At mdrun for the minimization, I get:

---
Program gmx mdrun, VERSION 5.1.2
Source code file: 
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
line: 276

Fatal error:
1 particles communicated to PME rank 3 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


This may be caused by the solvent replacement of genion by Na Cl:



Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
Will try to add 130 Na ions and 90 Cl ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 98254 elements
Group 1 ( DNA) has 1333 elements
Group 2 ( Water) has 96921 elements
Group 3 ( SOL) has 96921 elements
Group 4 ( non-Water) has 1333 elements
Select a group: 3
Selected 3: 'SOL'
Number of (3-atomic) solvent molecules: 32307
Replacing solvent molecule 3244 (atom 11065) with Na
Replacing solvent molecule 8993 (atom 28312) with Na
Replacing solvent molecule 7088 (atom 22597) with Na
Replacing solvent molecule 29442 (atom 89659) with Na
Replacing solvent molecule 30079 (atom 91570) with Na
Replacing solvent molecule 5128 (atom 16717) with Na
Replacing solvent molecule 10705 (atom 33448) with Na
Replacing solvent molecule 1418 (atom 5587) with Na
Replacing solvent molecule 6608 (atom 21157) with Na
Replacing solvent molecule 28124 (atom 85705) with Na
Replacing solvent molecule 5440 (atom 17653) with Na
Replacing solvent molecule 31518 (atom 95887) with Na
Replacing solvent molecule 16384 (atom 50485) with Na
Replacing solvent molecule 17675 (atom 54358) with Na
Replacing solvent molecule 23446 (atom 71671) with Na
Replacing solvent molecule 15659 (atom 48310) with Na
Replacing solvent molecule 18442 (atom 56659) with Na
Replacing solvent molecule 23777 (atom 72664) with Na
Replacing solvent molecule 5965 (atom 19228) with Na
Replacing solvent molecule 15375 (atom 47458) with Na
Replacing solvent molecule 30985 (atom 94288) with Na
Replacing solvent molecule 19076 (atom 58561) with Na
Replacing solvent molecule 18065 (atom 55528) with Na
Replacing solvent molecule 22711 (atom 69466) with Na
Replacing solvent molecule 27097 (atom 82624) with Na
Replacing solvent molecule 21561 (atom 66016) with Na
Replacing solvent molecule 18592 (atom 57109) with Na
Replacing solvent molecule 22174 (atom 67855) with Na
Replacing solvent molecule 17888 (atom 54997) with Na
Replacing solvent molecule 13005 (atom 40348) with Na
Replacing solvent molecule 3481 (atom 11776) with Na
Replacing solvent molecule 22603 (atom 69142) with Na
Replacing solvent molecule 9899 (atom 31030) with Na
Replacing solvent molecule 3438 (atom 11647) with Na
Replacing solvent molecule 12180 (atom 37873) with Na
Replacing solvent molecule 32219 (atom 97990) with Na
Replacing solvent molecule 23159 (atom 70810) with Na
Replacing solvent molecule 27929 (atom 85120) with Na


which then reflects on grompp as:



Setting the LD random seed to 3274024379
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA_chain_E'
Excluding 3 bonded neighbours molecule type 'DNA_chain_F'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
Excluding 1 bonded neighbours molecule type 'CL'
Warning: atom name 97595 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97596 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97597 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97598 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97599 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97600 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97601 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97602 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97603 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97604 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97605 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97606 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97607 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97608 in topol.top and dna_solv_NaCl.gro 

Re: [gmx-users] Genion

[Sergio Manzetti]

 97608 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97609 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97610 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97611 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97612 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97613 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97614 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
(more than 20 non-matching atom names) 

WARNING 1 [file topol.top, line 50]: 
220 non-matching atom names 
atom names from topol.top will be used 
atom names from dna_solv_NaCl.gro will be ignored 





Giving the mdrun problem.. 


Not sure how to get by this! 

Sergio 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul" <jalem...@vt.edu> 
To: "gmx-users" <gmx-us...@gromacs.org> 
Sent: Wednesday, June 21, 2017 4:53:59 PM 
Subject: Re: [gmx-users] Genion 

On 6/21/17 10:45 AM, Sergio Manzetti wrote: 
> Hi Justin, the sequence was: 
> 
> gmx editconf  
> 
> gmx solvate  
> 
> gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr 
> 
> gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA 
> -nname CL 
> 
> then: 
> 
> gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o 
> dna_solv_NaCl_EM 
> 
> gmx mdrun 
> 
> 
> This worked. 
> 
> Then for the sim: 
> 
> dna_solv_NaCl_EM.gro does not contain any ions. 
> 

You didn't pass topol_solvated.top to genion -p, so it did not update the 
number 
of ions. Your final call to grompp should have triggered an error because the 
contents of the system will not match, unless you did this manually. But again, 
it is *impossible* for mdrun to delete anything. So check the contents of your 
files carefully, even just in a text editor for coordinates and topology, to 
make sure you have what you think you have. 

-Justin 

-- 
== 

Justin A. Lemkul, Ph.D. 
Ruth L. Kirschstein NRSA Postdoctoral Fellow 

Department of Pharmaceutical Sciences 
School of Pharmacy 
Health Sciences Facility II, Room 629 
University of Maryland, Baltimore 
20 Penn St. 
Baltimore, MD 21201 

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul 

== 
-- 
Gromacs Users mailing list 

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! 

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Re: [gmx-users] Genion

[Sergio Manzetti]

Indeed, thanks: I did it manually. 

Will try updating the top with genion, 

Sergio 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul" <jalem...@vt.edu> 
To: "gmx-users" <gmx-us...@gromacs.org> 
Sent: Wednesday, June 21, 2017 4:53:59 PM 
Subject: Re: [gmx-users] Genion 

On 6/21/17 10:45 AM, Sergio Manzetti wrote: 
> Hi Justin, the sequence was: 
> 
> gmx editconf  
> 
> gmx solvate  
> 
> gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr 
> 
> gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA 
> -nname CL 
> 
> then: 
> 
> gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o 
> dna_solv_NaCl_EM 
> 
> gmx mdrun 
> 
> 
> This worked. 
> 
> Then for the sim: 
> 
> dna_solv_NaCl_EM.gro does not contain any ions. 
> 

You didn't pass topol_solvated.top to genion -p, so it did not update the 
number 
of ions. Your final call to grompp should have triggered an error because the 
contents of the system will not match, unless you did this manually. But again, 
it is *impossible* for mdrun to delete anything. So check the contents of your 
files carefully, even just in a text editor for coordinates and topology, to 
make sure you have what you think you have. 

-Justin 

-- 
== 

Justin A. Lemkul, Ph.D. 
Ruth L. Kirschstein NRSA Postdoctoral Fellow 

Department of Pharmaceutical Sciences 
School of Pharmacy 
Health Sciences Facility II, Room 629 
University of Maryland, Baltimore 
20 Penn St. 
Baltimore, MD 21201 

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul 

== 
-- 
Gromacs Users mailing list 

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! 

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Re: [gmx-users] Genion

[Sergio Manzetti]

Hi Justin, the sequence was: 

gmx editconf  

gmx solvate  

gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr 

gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA 
-nname CL 

then: 

gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o dna_solv_NaCl_EM 

gmx mdrun 


This worked. 

Then for the sim: 

dna_solv_NaCl_EM.gro does not contain any ions. 



Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul" <jalem...@vt.edu> 
To: "gmx-users" <gmx-us...@gromacs.org> 
Sent: Wednesday, June 21, 2017 4:44:16 PM 
Subject: Re: [gmx-users] Genion 

On 6/21/17 10:30 AM, Sergio Manzetti wrote: 
> Hello, genion worked, and grompp was used to run the output conf from genion. 
> Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no 
> longer contains the Na Cl ions added to the system. When setting up the 
> simulation, the input confout.gro has no Na Cl ions, and the procedure is 
> therefore not working. 
> 
> Why is this so? Does one have to do the genion procedure each time one wants 
> to use gromp with a new mdp file? 
> 

You run genion once to add ions to your system. Please provide the exact 
sequence of commands you're using. It's very hard to follow what you're 
describing. mdrun cannot delete anything, so "no longer contains the Na Cl 
ions" is impossible. Either the ions are there in the beginning or they're not. 
If you're using mdrun to run the .tpr file you're sending to genion, don't. 
There's no point. That .tpr file is not for a simulation, it's just for genion. 

-Justin 

-- 
== 

Justin A. Lemkul, Ph.D. 
Ruth L. Kirschstein NRSA Postdoctoral Fellow 

Department of Pharmaceutical Sciences 
School of Pharmacy 
Health Sciences Facility II, Room 629 
University of Maryland, Baltimore 
20 Penn St. 
Baltimore, MD 21201 

jalem...@outerbanks.umaryland.edu | (410) 706-7441 
http://mackerell.umaryland.edu/~jalemkul 

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Re: [gmx-users] Genion

[Justin Lemkul]

On 6/21/17 10:45 AM, Sergio Manzetti wrote:

Hi Justin, the sequence was:

gmx editconf 

gmx solvate 

gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr

gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA 
-nname CL

then:

gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o dna_solv_NaCl_EM

gmx mdrun


This worked.

Then for the sim:

dna_solv_NaCl_EM.gro does not contain any ions.



You didn't pass topol_solvated.top to genion -p, so it did not update the number 
of ions.  Your final call to grompp should have triggered an error because the 
contents of the system will not match, unless you did this manually.  But again, 
it is *impossible* for mdrun to delete anything.  So check the contents of your 
files carefully, even just in a text editor for coordinates and topology, to 
make sure you have what you think you have.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Genion

[Justin Lemkul]

On 6/21/17 10:30 AM, Sergio Manzetti wrote:

Hello, genion worked, and grompp was used to run the output conf from genion. 
Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no 
longer contains the Na Cl ions added to the system. When setting up the 
simulation, the input confout.gro has no Na Cl ions, and the procedure is 
therefore not working.

Why is this so? Does one have to do the genion procedure each time one wants to 
use gromp with a new mdp file?



You run genion once to add ions to your system.  Please provide the exact 
sequence of commands you're using.  It's very hard to follow what you're 
describing.  mdrun cannot delete anything, so "no longer contains the Na Cl 
ions" is impossible.  Either the ions are there in the beginning or they're not. 
 If you're using mdrun to run the .tpr file you're sending to genion, don't. 
There's no point.  That .tpr file is not for a simulation, it's just for genion.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Genion

[Sergio Manzetti]

Hello, genion worked, and grompp was used to run the output conf from genion. 
Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no 
longer contains the Na Cl ions added to the system. When setting up the 
simulation, the input confout.gro has no Na Cl ions, and the procedure is 
therefore not working. 

Why is this so? Does one have to do the genion procedure each time one wants to 
use gromp with a new mdp file? 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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Re: [gmx-users] genion -conc give the wrong number of multi-valent counter ion

[Mark Abraham]

Hi,

In general, run "gmx help tool" to see how the tool should be run, here to
see that there's an option for you to choose a non-default charge

Mark

On Fri, 16 Jun 2017 14:21 Justin Lemkul  wrote:

>
>
> On 6/16/17 7:14 AM, Quyen V. Vu wrote:
> > Dear GMX developer,
> > I don't know this mailing list is suitable for posting issue or not, if
> > not- forgive me.
> >
> > I want to report about gmx genion module
> >
> > If i want to add concentration of salt by -conc option, it just correct
> for
> > monovalent salt (eg. NACL).
> >
> > For multivalent salt(MGCL2), if I use -pname MG -nname CL -conc X
> -neutral
> > , it wil treat MG as monovanlent cation and give the wrong number of ions
> > add into my system, so  I have to use -np and -nn option to get correct
> the
> > number of ions.
> >
>
> If you set the correct value of -pq then you'll get the right result.
> genion
> defaults to assuming everything is monovalent and if that's not the case,
> you
> have to provide correct instructions via the command line.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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Re: [gmx-users] genion -conc give the wrong number of multi-valent counter ion

[Justin Lemkul]

On 6/16/17 7:14 AM, Quyen V. Vu wrote:

Dear GMX developer,
I don't know this mailing list is suitable for posting issue or not, if
not- forgive me.

I want to report about gmx genion module

If i want to add concentration of salt by -conc option, it just correct for
monovalent salt (eg. NACL).

For multivalent salt(MGCL2), if I use -pname MG -nname CL -conc X -neutral
, it wil treat MG as monovanlent cation and give the wrong number of ions
add into my system, so  I have to use -np and -nn option to get correct the
number of ions.



If you set the correct value of -pq then you'll get the right result.  genion 
defaults to assuming everything is monovalent and if that's not the case, you 
have to provide correct instructions via the command line.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] genion -conc give the wrong number of multi-valent counter ion

[Quyen V. Vu]

Dear GMX developer,
I don't know this mailing list is suitable for posting issue or not, if
not- forgive me.

I want to report about gmx genion module

If i want to add concentration of salt by -conc option, it just correct for
monovalent salt (eg. NACL).

For multivalent salt(MGCL2), if I use -pname MG -nname CL -conc X -neutral
, it wil treat MG as monovanlent cation and give the wrong number of ions
add into my system, so  I have to use -np and -nn option to get correct the
number of ions.

Best regards
Quyen


Virus-free.
www.avast.com

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Re: [gmx-users] Genion error

[‪Mohammad Roostaie‬ ‪]

Thank you very much Justin. It is good now.
Best,Mohammad

  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Monday, 29 May 2017, 23:40:06
 Subject: Re: [gmx-users] Genion error
   


On 5/29/17 4:35 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Thank you Justin. Here is the link to access the topology 
> file:https://www.dropbox.com/sh/x58tzpmg0vzkbtg/AADH_efF_s8jKx4OaHN8a7IPa?dl=0
> 
> By the way, I do not know about your advice. Can you please give me the link?

It's somewhere in the archive.  Run the topology through dos2unix and always 
make sure to use a plain text editor.  See if that works.

-Justin

> Kind regards,Mohammad
> 
>        From: Justin Lemkul <jalem...@vt.edu>
>  To: gmx-us...@gromacs.org
>  Sent: Monday, 29 May 2017, 0:21:10
>  Subject: Re: [gmx-users] Genion error
>    
> 
> 
> On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>> Hi All, when I wanted to add ions to the system, I got this error:
>> Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section 
>> of file 'gr.top'For more information and tips for troubleshooting, please 
>> check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
>> However, there is 'SOL' molecule type in the [ molecules ] section of the 
>> topology file. Can you please help me to solve this problem?
> 
> Upload your topology to a file-sharing service and provide the URL to access 
> it.
>    There's no way to know what's going on (and I recall giving some previous
> advice about line endings - have you checked this?)
> 
> -Justin
> 

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Genion error

[Justin Lemkul]

On 5/29/17 4:35 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Thank you Justin. Here is the link to access the topology 
file:https://www.dropbox.com/sh/x58tzpmg0vzkbtg/AADH_efF_s8jKx4OaHN8a7IPa?dl=0

By the way, I do not know about your advice. Can you please give me the link?


It's somewhere in the archive.  Run the topology through dos2unix and always 
make sure to use a plain text editor.  See if that works.


-Justin


Kind regards,Mohammad

   From: Justin Lemkul <jalem...@vt.edu>
  To: gmx-us...@gromacs.org
  Sent: Monday, 29 May 2017, 0:21:10
  Subject: Re: [gmx-users] Genion error




On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Hi All, when I wanted to add ions to the system, I got this error:
Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of 
file 'gr.top'For more information and tips for troubleshooting, please check 
the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
However, there is 'SOL' molecule type in the [ molecules ] section of the 
topology file. Can you please help me to solve this problem?


Upload your topology to a file-sharing service and provide the URL to access it.
   There's no way to know what's going on (and I recall giving some previous
advice about line endings - have you checked this?)

-Justin



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Genion error

[‪Mohammad Roostaie‬ ‪]

Thank you Justin. Here is the link to access the topology 
file:https://www.dropbox.com/sh/x58tzpmg0vzkbtg/AADH_efF_s8jKx4OaHN8a7IPa?dl=0

By the way, I do not know about your advice. Can you please give me the link?
Kind regards,Mohammad

  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Monday, 29 May 2017, 0:21:10
 Subject: Re: [gmx-users] Genion error
   


On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi All, when I wanted to add ions to the system, I got this error:
> Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section 
> of file 'gr.top'For more information and tips for troubleshooting, please 
> check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
> However, there is 'SOL' molecule type in the [ molecules ] section of the 
> topology file. Can you please help me to solve this problem?

Upload your topology to a file-sharing service and provide the URL to access 
it. 
  There's no way to know what's going on (and I recall giving some previous 
advice about line endings - have you checked this?)

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Genion error

[Justin Lemkul]

On 5/28/17 3:43 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Hi All, when I wanted to add ions to the system, I got this error:
Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of 
file 'gr.top'For more information and tips for troubleshooting, please check 
the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
However, there is 'SOL' molecule type in the [ molecules ] section of the 
topology file. Can you please help me to solve this problem?


Upload your topology to a file-sharing service and provide the URL to access it. 
 There's no way to know what's going on (and I recall giving some previous 
advice about line endings - have you checked this?)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Genion error

[‪Mohammad Roostaie‬ ‪]

Hi All, when I wanted to add ions to the system, I got this error:
Fatal error:No line with moleculetype 'SOL' found the [ molecules ] section of 
file 'gr.top'For more information and tips for troubleshooting, please check 
the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
However, there is 'SOL' molecule type in the [ molecules ] section of the 
topology file. Can you please help me to solve this problem?
Thanks,Mohammad
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Re: [gmx-users] genion command

[Justin Lemkul]

On 5/16/17 12:55 AM, Saumyak Mukherjee wrote:

Hello Diana,

You may try using the -conc flag in genion program to specify your salt
concentration, along with -nname and -pname flags.



The -nname and -pname options are irrelevant here.

If there are fewer than 1000 waters in the system, I doubt the number of ions 
has been calculated correctly, though.  Compare with -conc 0.6 to see if the 
math is right, and make sure that the solvent is actually being replaced, not 
anything else.


-Justin


Best wishes,
Saumyak

On 16 May 2017 at 10:18, diana p  wrote:


Dear gmx users,
I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use
genion command and add 720 CL and 360 Ca ions respectively to the system of
pure 12568 water molecules.But on running the command genion I get error
message:

Program genion, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c,
line:
89
Fatal error:
No more replaceable solvent!

How should I add ions in the system.I would be more than pleased if someone
could guid me.
Thank You in advance
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==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
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Re: [gmx-users] genion command

[Saumyak Mukherjee]

Hello Diana,

You may try using the -conc flag in genion program to specify your salt
concentration, along with -nname and -pname flags.

Best wishes,
Saumyak

On 16 May 2017 at 10:18, diana p  wrote:

> Dear gmx users,
> I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use
> genion command and add 720 CL and 360 Ca ions respectively to the system of
> pure 12568 water molecules.But on running the command genion I get error
> message:
>
> Program genion, VERSION 4.6.5
> Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c,
> line:
> 89
> Fatal error:
> No more replaceable solvent!
>
> How should I add ions in the system.I would be more than pleased if someone
> could guid me.
> Thank You in advance
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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[gmx-users] genion command

[diana p]

Dear gmx users,
I want to simulate 0.6M CaCL2 aqueous solution. To add the ions I use
genion command and add 720 CL and 360 Ca ions respectively to the system of
pure 12568 water molecules.But on running the command genion I get error
message:

Program genion, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_genion.c, line:
89
Fatal error:
No more replaceable solvent!

How should I add ions in the system.I would be more than pleased if someone
could guid me.
Thank You in advance
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Re: [gmx-users] genion

[Justin Lemkul]

On 8/15/16 4:11 AM, f.namazi...@sci.ui.ac.ir wrote:

Hi every body;
Why we should neutralise net charge of the simulation system?


To properly answer your question, we must approach it with a bit more nuance.

One typically neutralizes the net charge of a condensed-phase system for two 
reasons, one physical and one algorithmic.  First, in e.g. aqueous solution, 
positives don't exist without negatives.  That's just fundamental physics.  If a 
species ionizes in solution, its corresponding counterion is generated.  Second, 
the de facto standard for computing electrostatic interactions in an MD 
simulation using PBC is PME, which requires a net-neutral simulation system. 
One does *not* have to add counterions to achieve net neutrality, as the PME 
algorithm itself contibutes a uniform background plasma to neutralize the 
charge.  The problem is that, in heterogeneous systems, this uniform background 
charge leads to artifactual behavior.  Most all biomolecular simulations are 
heterogeneous, so it is unwise to rely on PME itself to account for this effect. 
 So the very simple solution is to add counterions.  Generally, one should add 
some additional ions to mimic in vitro or in vivo conditions (e.g. for 
biomolecules) but the exact approach depends on what is being studied.


There are other systems, for instance an ionized protein in vacuo, for which you 
would not add counterions (there's nowhere to add them, really).  But in these 
cases, you wouldn't be using PME, anyway.


So the real answer depends on what you are doing.  It is commonly accepted that 
with PME, the easiest thing to do is add a couple of ions to balance out the charge.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] genion

[Nikhil Maroli]

Depends on the simulation but in general, most of the biological systems
occur at natural pH which around is 7.4, So mimicking the exact biological
system we are neutralising the system.
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Re: [gmx-users] genion

[Alexander Alexander]

Hi Farzaneh,

If I am not entirely wrong;
Otherwise, the tiny amount of charge in a single box would be huge in the
calculation because of PBC(periodic boundary condition) and a coulomb
explosion would happen.

Cheers,
Alex

On Mon, Aug 15, 2016 at 10:11 AM,  wrote:

> Hi every body;
> Why we should neutralise net charge of the simulation system?
> Regards.
> Farzaneh
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[gmx-users] genion

[f . namazifar]

Hi every body;
Why we should neutralise net charge of the simulation system?
Regards.
Farzaneh
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Re: [gmx-users] genion with Na or Ca

[Turgay Cakmak]

Thank you for your useful replies.
Turgay

2016-01-12 23:38 GMT+02:00 VITALY V. CHABAN :

> Ca(2+) will block one of your binding sites, if you care.
>
>
>
>
>
> On Tue, Jan 12, 2016 at 6:19 AM, Turgay Cakmak 
> wrote:
>
> > Hi all,
> >
> >
> > I have a quick question about neutralizing the system. I have a solvated
> > system that contains a charged protein of -2q. Is there a major
> difference
> > betwen adding 2 Na ions and a single  Ca ion to neutralize the system
> > (using genion)?
> >
> >
> > Thanks in advance,
> >
> > Turgay
> > --
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Re: [gmx-users] genion with Na or Ca

[VITALY V. CHABAN]

Ca(2+) will block one of your binding sites, if you care.





On Tue, Jan 12, 2016 at 6:19 AM, Turgay Cakmak 
wrote:

> Hi all,
>
>
> I have a quick question about neutralizing the system. I have a solvated
> system that contains a charged protein of -2q. Is there a major difference
> betwen adding 2 Na ions and a single  Ca ion to neutralize the system
> (using genion)?
>
>
> Thanks in advance,
>
> Turgay
> --
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Re: [gmx-users] genion with Na or Ca

[Smith, Micholas D.]

At low concentrations (just a single Ca2+) you shouldn't expect any huge 
differences, though the Ca2+ may stick around the protein surface a little bit 
longer than the Na+ ions which may alter how one of the charged residues is 
hydrated. If the protein is of a modest size (not a small fragment), than any 
modifications to the hydration of a single residue likely will not be a huge 
driving factor to your dynamics...though this is not guaranteed.  

When in doubt, run both simulation conditions and compare.

-Micholas

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: Tuesday, January 12, 2016 7:41 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] genion with Na or Ca

On 1/12/16 3:19 AM, Turgay Cakmak wrote:
> Hi all,
>
>
> I have a quick question about neutralizing the system. I have a solvated
> system that contains a charged protein of -2q. Is there a major difference
> betwen adding 2 Na ions and a single  Ca ion to neutralize the system
> (using genion)?
>

For the purposes of neutralization, probably not, but note that additive force
fields do not deal well with divalent ions.  Na+ or K+ are preferable if only
being used for simple balancing of charge.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] genion with Na or Ca

[Justin Lemkul]

On 1/12/16 3:19 AM, Turgay Cakmak wrote:

Hi all,


I have a quick question about neutralizing the system. I have a solvated
system that contains a charged protein of -2q. Is there a major difference
betwen adding 2 Na ions and a single  Ca ion to neutralize the system
(using genion)?



For the purposes of neutralization, probably not, but note that additive force 
fields do not deal well with divalent ions.  Na+ or K+ are preferable if only 
being used for simple balancing of charge.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] genion problem

[Golnaz Roudsari]

Dear all
I want to use bromide for neutralize my system. I wrote genion -s ions.tpr
-c file.gro -p topol.top -pname K -nname BR -nn 24. After I cheked it the
gromacs read Boron intead of bromide. I wrote command -nname BR -nn 24. and
I did not use K but in all cases my output was boron and I did not see any
Bromide.
I would appreciate any suggestion.
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Re: [gmx-users] genion problem

[Justin Lemkul]

On 10/5/15 2:26 AM, Golnaz Roudsari wrote:

Dear all
I want to use bromide for neutralize my system. I wrote genion -s ions.tpr
-c file.gro -p topol.top -pname K -nname BR -nn 24. After I cheked it the
gromacs read Boron intead of bromide. I wrote command -nname BR -nn 24. and
I did not use K but in all cases my output was boron and I did not see any
Bromide.


Something doesn't add up.  But the only force field that supports Br- is 
OPLS-AA, so if you're using any other force field, whatever genion writes may 
not be correct or even supported by the force field.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] genion error sol not continuous

[James Lord]

Hi Justin,
Thanks for your email. I have modified it and the topology looks fine to me
or at least I can't see any problem with it but still genion does not like
it? Would please have a look?
https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing
https://drive.google.com/file/d/0B0YMTXH1gmQsMjlMTlNPeWJqdkk/view?usp=sharing

Thanks
James

On Fri, May 15, 2015 at 4:36 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/14/15 1:25 AM, James Lord wrote:

 Hi all,
 I am trying to neutralize this system (1HFX.gro) and genion is complaining
 about solvent not being continuous,then I made the 1HFX_modified.gro in
 which
 I have replaced HOH from 1HFX.gro with SOL and cut paste them at the end
 of
 the file. I am expecting gromacs to do the reordering for SOL. Am I
 missing
 anything?


 The topology needs to be modified in a similar manner.  IIRC it is
 topological continuity that genion checks.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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[gmx-users] genion question

[ANDRES ADOLFO ORTEGA GUERRERO]

Hi Dear Gromacs Users,

 I have a doubt , if i need a electrolyte concentration of 150mM of ions of
NA and CL

the right comand is

genion -s file.tpr -o topol.top -nname CL -pname NA -neutral -conc 0.150 -o
out.gro ?

thanks in advance
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Re: [gmx-users] genion question

[Justin Lemkul]

On 7/23/14, 5:18 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:

Hi Dear Gromacs Users,

  I have a doubt , if i need a electrolyte concentration of 150mM of ions of
NA and CL

the right comand is

genion -s file.tpr -o topol.top -nname CL -pname NA -neutral -conc 0.150 -o
out.gro ?



Yes.  You can confirm the outcome with simple calculations from general 
chemistry.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] genion

[Que Pasa]

If you want a simulation w/o Zinc as a control then build a new system/pdb
w/o it (just delete the Zn line)  rather than doing something exotic like
turning off its charge. Turning off charges (and van der Waals parameters)
is an approach more suitable for alchemical calculations
http://www.alchemistry.org/wiki/Main_Page . Avoid jumping into these unless
you know exactly what you are doing.


On Fri, May 23, 2014 at 12:21 PM, elham tazikeh elham.tazi...@gmail.comwrote:

 dear users
 i studied on amyloid beta peptide with zinc cation and
 i choosed 1ze9 as my pdb file
 can i assume Zn without charge in  protein simulation alone,
 or i have to using the amyloid beta peptide alone as pdb
 for instance,1iyt???
 best wishes
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[gmx-users] genion

[elham tazikeh]

dear users
i studied on amyloid beta peptide with zinc cation and
i choosed 1ze9 as my pdb file
can i assume Zn without charge in  protein simulation alone,
or i have to using the amyloid beta peptide alone as pdb
for instance,1iyt???
best wishes
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Re: [gmx-users] genion

[Justin Lemkul]

On 3/16/14, 9:49 AM, Andrew Bostick wrote:

Dear Kalyan

Thanks for your reply

I want to use Zn2+ ions with my protein.

There is Zn2+ ions in atomtypes.atp file of opls force field. But there is
not Zn2+ ions in ions.itp file of of opls force field.

Based on your answer, now, I can not use Zn2+ ions in genion tool.

Is it true? But I used

genion -s ions.tpr -o mol.gro -p topol.top -np 2 -pname ZN -pq +2

and I did not encountered with error and solvent molecules replaced with
Zn2+ ions.

I confused. Please give me more explanations.



genion does not read ions.itp to understand which ions it can and can't add.  It 
does what you tell it.  You can name your monovalent ions anything you like at 
this stage; the only thing that matters is that the name supplied corresponds to 
some known [moleculetype] in that force field - either in ions.itp or in an .itp 
file of your own creation.  If there is no ZN [moleculetype] anywhere, grompp 
will die with a fatal error.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] genion

[Andrew Bostick]

Dear gromacs users

In genion tool of gromacs, there are only Na and Cl ions. I want to add
Zn2+ ions to my system.

How to add these ions with special concentration?

Any help will highly appreciated
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Re: [gmx-users] Genion command not working

[srinivasa rao lanke]

Thank you very much your reply
its working fine if i decrease distance

thank you

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