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:
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 mail
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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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 i
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
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
/ | Nanofactory
] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]
From: "Mark Abraham"
To: "gmx-users"
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
/ | Nanofactory
] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]
From: "Justin Lemkul"
To: "gmx-users"
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.
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 ]
>
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 alread
x-users"
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:
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, VERSI
emkul"
To: "gmx-users"
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 f
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/gro
"Justin Lemkul"
To: "gmx-users"
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 g
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"
To: "gmx-users"
Sent: Wednesday, June 21, 2017 4:53:59 PM
Subject: Re: [gmx-users] Genion
M
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 th
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 e
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
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
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 mailin
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).
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 -pna
Thank you very much Justin. It is good now.
Best,Mohammad
From: Justin Lemkul
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
n 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
To: gmx-us...@gromacs.org
Sent: Monday, 29 May 2017, 0:21:10
Subject: Re: [gmx-users] Genion error
On 5/28
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
>
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
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,
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 doub
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
> genio
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
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
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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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 shoul
Hi every body;
Why we should neutralise net charge of the simulation system?
Regards.
Farzaneh
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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.
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 addin
t: 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
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
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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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 bu
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 no
Thanks Justin problem solved.
Cheers
James
On Sat, May 16, 2015 at 9:21 AM, Justin Lemkul wrote:
>
>
> On 5/15/15 4:53 PM, James Lord wrote:
>
>> 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
On 5/15/15 4:53 PM, James Lord wrote:
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
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
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 expec
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.
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 c
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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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.alchemi
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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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 Zn
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
Dear Andrew,
First of all you just have a look at the "*Ions.itp" *file, which exists in
"gromacs-4.5.2/share/top/(any forcefield you are working with)" in your
installed directory.
There you will find all types of *Ions* we can use.
Regarding *genion tool, *this command should work:
"*genion -
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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Thank you very much your reply
its working fine if i decrease distance
thank you
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Hi Srinivas,
Have you tried my suggestion?
Cheers,
Tsjerk
On Fri, Jan 24, 2014 at 7:45 AM, srinivasa rao lanke
wrote:
> IS IT this problem solved or not???
>
>
> I am also pacing same problem.
>
>
>
>
>
> srinivas
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Geni
IS IT this problem solved or not???
I am also pacing same problem.
srinivas
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