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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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
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
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
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 i
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
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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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 ge
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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View this message in context:
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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,
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
-
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
--
gmx-users mailing
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
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Lab
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 -
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
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 r
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 wate
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 list
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
> tr
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
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
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
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