Re: [gmx-users] dielectric constant -reg

[Mark Abraham]

Hi,

You haven't described what you're doing in enough detail for anybody to be
able to suggest where you or the code might be doing something wrong.

Mark

On Tue, Sep 12, 2017 at 12:36 PM Meagha ramana kumar 
wrote:

> hi mark,
>
> Same doubt in the following thread.
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-May/106078.html
>
> with epsilon_-surface =0, simulation runs fine. The problem starts when I
> give it a value. My model has only protein and doesn't have anything other
> than that.
> Moreover, i have read the .mdp file, as you have mentioned in the previous
> threads.
>
>
> thank u
> Meagha
>
> On Mon, Sep 11, 2017 at 9:53 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Clearly the .mdp file changes you say you are making aren't showing up
> > later in wherever you are observing a 1.12, but we'll need to see a lot
> > more detail of your process - e.g. command lines with the file names - to
> > suggest what might be wrong. That means you need to be able to copy and
> > paste them from a terminal or script, or you won't generally be able to
> > reconcile what you think you did with what you actually did.
> >
> > Mark
> >
> > On Mon, Sep 11, 2017 at 9:51 AM Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Change the mdp file and use that file to make a new tpr file and that
> the
> > > file to run a simulation.
> > >
> > > Mark
> > >
> > > On Mon, 11 Sep 2017 08:21 Meagha ramana kumar 
> wrote:
> > >
> > >> Hi gmx-users,
> > >>
> > >> My problem may sound silly, but please help me with it. I know how to
> > >> change dielectric constant for simulation. Yes I have read all the
> > previous
> > >> thread reading this and no one provided straight answer to this. I am
> > using
> > >> PME. I tried changing all the epsilon values but nothing helped and I
> > get
> > >> 1.12. will be thankful , if you guys help me out.
> > >>
> > >> Thank you
> > >> Meagha
> > >>
> > >>
> > >> Sent from Mail for Windows 10
> > >>
> > >> --
> > >> 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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> > >>
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> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> > >
> > --
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Re: [gmx-users] dielectric constant -reg

[Meagha ramana kumar]

hi mark,

Same doubt in the following thread.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-May/106078.html

with epsilon_-surface =0, simulation runs fine. The problem starts when I
give it a value. My model has only protein and doesn't have anything other
than that.
Moreover, i have read the .mdp file, as you have mentioned in the previous
threads.


thank u
Meagha

On Mon, Sep 11, 2017 at 9:53 PM, Mark Abraham 
wrote:

> Hi,
>
> Clearly the .mdp file changes you say you are making aren't showing up
> later in wherever you are observing a 1.12, but we'll need to see a lot
> more detail of your process - e.g. command lines with the file names - to
> suggest what might be wrong. That means you need to be able to copy and
> paste them from a terminal or script, or you won't generally be able to
> reconcile what you think you did with what you actually did.
>
> Mark
>
> On Mon, Sep 11, 2017 at 9:51 AM Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Change the mdp file and use that file to make a new tpr file and that the
> > file to run a simulation.
> >
> > Mark
> >
> > On Mon, 11 Sep 2017 08:21 Meagha ramana kumar  wrote:
> >
> >> Hi gmx-users,
> >>
> >> My problem may sound silly, but please help me with it. I know how to
> >> change dielectric constant for simulation. Yes I have read all the
> previous
> >> thread reading this and no one provided straight answer to this. I am
> using
> >> PME. I tried changing all the epsilon values but nothing helped and I
> get
> >> 1.12. will be thankful , if you guys help me out.
> >>
> >> Thank you
> >> Meagha
> >>
> >>
> >> Sent from Mail for Windows 10
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] dielectric constant -reg

[Mark Abraham]

Hi,

Clearly the .mdp file changes you say you are making aren't showing up
later in wherever you are observing a 1.12, but we'll need to see a lot
more detail of your process - e.g. command lines with the file names - to
suggest what might be wrong. That means you need to be able to copy and
paste them from a terminal or script, or you won't generally be able to
reconcile what you think you did with what you actually did.

Mark

On Mon, Sep 11, 2017 at 9:51 AM Mark Abraham 
wrote:

> Hi,
>
> Change the mdp file and use that file to make a new tpr file and that the
> file to run a simulation.
>
> Mark
>
> On Mon, 11 Sep 2017 08:21 Meagha ramana kumar  wrote:
>
>> Hi gmx-users,
>>
>> My problem may sound silly, but please help me with it. I know how to
>> change dielectric constant for simulation. Yes I have read all the previous
>> thread reading this and no one provided straight answer to this. I am using
>> PME. I tried changing all the epsilon values but nothing helped and I get
>> 1.12. will be thankful , if you guys help me out.
>>
>> Thank you
>> Meagha
>>
>>
>> Sent from Mail for Windows 10
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
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Re: [gmx-users] dielectric constant -reg

[Mark Abraham]

Hi,

Change the mdp file and use that file to make a new tpr file and that the
file to run a simulation.

Mark

On Mon, 11 Sep 2017 08:21 Meagha ramana kumar  wrote:

> Hi gmx-users,
>
> My problem may sound silly, but please help me with it. I know how to
> change dielectric constant for simulation. Yes I have read all the previous
> thread reading this and no one provided straight answer to this. I am using
> PME. I tried changing all the epsilon values but nothing helped and I get
> 1.12. will be thankful , if you guys help me out.
>
> Thank you
> Meagha
>
>
> Sent from Mail for Windows 10
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] dielectric constant -reg

[Meagha ramana kumar]

Hi gmx-users,

My problem may sound silly, but please help me with it. I know how to change 
dielectric constant for simulation. Yes I have read all the previous thread 
reading this and no one provided straight answer to this. I am using PME. I 
tried changing all the epsilon values but nothing helped and I get 1.12. will 
be thankful , if you guys help me out.

Thank you 
Meagha


Sent from Mail for Windows 10

-- 
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