Hi,
I am a little embarrassed to ask this, especially because there are many
posts related to the term "inconsistent shift." Unfortunately, I still
cannot seem to find the answer to my question.
What is an inconsistent shift? Is it related to constraints or restraints?
Or is it more related to
Hi Justin,
Really appreciate your help. I have solved the problem following your
suggestion :)
I love this community~
2012/3/7 Justin A. Lemkul
>
>
> ming ma wrote:
>
>> Hi,
>>
>> Thanks for looking at this email. Before I asked this question, I have
>> read most of the related topics in gromac
ming ma wrote:
Hi,
Thanks for looking at this email. Before I asked this question, I have
read most of the related topics in gromacs's mailing list, but still
can't solve it.
When I was trying to do energy minimization of graphene with pbc, I got
several messages "there are # inconsistent s
Hi,
Thanks for looking at this email. Before I asked this question, I have read
most of the related topics in gromacs's mailing list, but still can't solve
it.
When I was trying to do energy minimization of graphene with pbc, I got
several messages "there are # inconsistent shifts, check your topo
Problem is solved.
Thanks,
Po-Han
Date: Fri, 16 Jan 2009 09:31:28 +0100
From: Berk Hess
Subject: RE: [gmx-users] Inconsistent shifts Problem when using g_rdf
To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset="windows-1252"
> Date: Fri, 16 J
> Date: Fri, 16 Jan 2009 09:06:43 +0100
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Inconsistent shifts Problem when using g_rdf
>
> Lin, Pohan wrote:
> > I am running NPT simulations by using Parrinello-Rahman pressure
>
Lin, Pohan wrote:
I am running NPT simulations by using Parrinello-Rahman pressure
coupling on Gromacs 3.3.3. My system contains epoxy and cross-linker
molecules. By modifying the topology file (add bond, angle, torsion
terms in topology), all the molecules are connected together to be an
hu
I am running NPT simulations by using Parrinello-Rahman pressure coupling on
Gromacs 3.3.3. My system contains epoxy and cross-linker molecules. By
modifying the topology file (add bond, angle, torsion terms in topology), all
the molecules are connected together to be an huge polymeric molecul
Hi
I am a new Gromacs user.I am trying to study the adsorption of proteins
on graphite surface.In mdp file I took the option pbc=full. When I am
running a simulation for 5 ns, I am getting the output with out any
warning. But when I am analysing the results using h_bond , g_gyrate and
do_dssp, I a
Bert wrote:
Hi all,
I use pbc=full in my system, and all runs are ok except for the
"inconsistent shifts" warnings when I use some analysis tools, such as
g_density, g_densmap, etc. I have searched the whole list related to
this problem, and I doubt several analysis tools are not coded with
Hi all,
I use pbc=full in my system, and all runs are ok except for the
"inconsistent shifts" warnings when I use some analysis tools, such as
g_density, g_densmap, etc. I have searched the whole list related to this
problem, and I doubt several analysis tools are not coded with consideration
of f
Mitchell Stanton-Cook wrote:
Hi David,
Using GMX3.2.2 unfortunately introduces more problems. See my message on
the 10/08/2007. I recently came across a post suggesting this is due to
a error in Reaction Field, however I believe that this problem me be a
little deeper.
Problems reported on th
Hi David,
Using GMX3.2.2 unfortunately introduces more problems. See my message on
the 10/08/2007. I recently came across a post suggesting this is due to
a error in Reaction Field, however I believe that this problem me be a
little deeper.
I have come across inconsistent shifts before - it
Mitchell Stanton-Cook wrote:
I have performed a search of the archive, but am yet to understand the
meaning of "inconsistent shifts".
I am using GMX331.
I am simulating a protein structure solved by NMR.
I have performed EM, PR and run the structure out for 500ps of MD before
beginning my pr
I have performed a search of the archive, but am yet to understand the
meaning of "inconsistent shifts".
I am using GMX331.
I am simulating a protein structure solved by NMR.
I have performed EM, PR and run the structure out for 500ps of MD before
beginning my production runs.
I am using bo
: Discussion list for GROMACS users
Subject: Re: [gmx-users] Inconsistent shifts using multiple bonds type 6
Date: Tue, 06 Mar 2007 12:44:16 +
Hi Berk,
Thanks for your reply. Yes the latter is the case in my system so i will
use pbc=full or remove these 'bonds' that i know will be g
From: TJ Piggot <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Inconsistent shifts using multiple bonds type 6
Date: Tue, 06 Mar 2007 12:44:16 +
Hi Berk,
Thanks for your reply. Yes the latter is th
From: TJ Piggot <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Inconsistent shifts using multiple bonds type 6
Date: Tue, 06 Mar 2007 00:22:00 +
Hi Mark thanks for your reply,
I'm not sur
From: TJ Piggot <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Inconsistent shifts using multiple bonds type 6
Date: Tue, 06 Mar 2007 00:22:00 +
Hi Mark thanks for your reply,
I'm not sure the
Hi Mark thanks for your reply,
I'm not sure the problem is that these restraints are inappropriate, but
the problem might be the sheer number. For example if i restrain a fairly
large number of atom distances (say 100 Calpha distances) to the same
length they are in the structure after minimis
> Hello all,
>
> I am trying to apply a set of harmonic distance restraints between pairs
> of
> protein atoms in my system, which is protein/ligand/water/ions in a
> periodic box.
>
> The way i am doing this is to use the bond type 6 and to add these bonds
> at
> the end of the [bonds] section in
Hello all,
I am trying to apply a set of harmonic distance restraints between pairs of
protein atoms in my system, which is protein/ligand/water/ions in a
periodic box.
The way i am doing this is to use the bond type 6 and to add these bonds at
the end of the [bonds] section in my topology f
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