Hello,
I am willing to study the free energy of binding of a cation (Ca++) to
the protein and I am following the free energy tutorial
provided by Justin
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy
).
Please let me know whether the settings for this type of s
>Hi Michiel,
>
>I disagree, and so does semantics. The cumulative variance of a pc is the
>variance of it plus the sum of the preceding ones. You're talking about the
>cumulative fraction of the total variance.
You are right about the proper word usage. It seemed to me from his question,
the use
Excuse me, I did all of examples in my system with different molecules (even
water alone) and with different force fields and I took this warning for all of
them by doing genbox command!!!
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom name
Hi users,
i would like to know which version of gromacs would be compatible with the
cluster architecture =
Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005
ppc64 ppc64 ppc64 GNU/Linux
And which gromacs version would be compatible with the mpi version =
mpich-1.2.7
Thank
Hi Michiel,
I disagree, and so does semantics. The cumulative variance of a pc is the
variance of it plus the sum of the preceding ones. You're talking about the
cumulative fraction of the total variance.
Cheers,
Tajerk
On Dec 16, 2011 12:07 AM, "Niesen, Michiel" wrote:
>Date: Thu, 15 Dec 201
On 16/12/2011 10:47 AM, Sanku M wrote:
Hi,
I am wondering whether someone can suggest a reference paper based
on which all gromacs principal component analysis (PCA) analysis ( i.e
g_covar and g_anaeig tools) tools are based . Or, any other review
articles on PCA analysis is based will als
Hi,
I am wondering whether someone can suggest a reference paper based on which
all gromacs principal component analysis (PCA) analysis ( i.e g_covar and
g_anaeig tools) tools are based . Or, any other review articles on PCA
analysis is based will also be useful.
Thanks
Sanku--
gmx-users ma
On 16/12/2011 7:22 AM, lq z wrote:
Dear GMXers,
I'm trying to manually add two sets of Urey-Bradley terms to the
topology file (in [angle] entry with type 5). However, it seems it is
not allowed. I got the following error:
Incorrect number of parameters - found 8, expected 4 or 4 for U-B.
I
Thanks Micheal for pointing out the mistake
On Fri, Dec 16, 2011 at 4:20 AM, Niesen, Michiel wrote:
> >Date: Thu, 15 Dec 2011 15:11:12 -0500
> >From: "R.S.K.Vijayan"
> >Subject: [gmx-users] Eigenvalue values from PCA (a general question)
> >To: gmx-users@gromacs.org
> >Message-ID:
> > <
>
>Date: Thu, 15 Dec 2011 15:11:12 -0500
>From: "R.S.K.Vijayan"
>Subject: [gmx-users] Eigenvalue values from PCA (a general question)
>To: gmx-users@gromacs.org
>Message-ID:
>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi all
>
>I have a query about the eigenvalue values obtained fro
Thanks Tsjerk
On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar wrote:
> Hi Vijayan.R,
>
> Not really. NMA also assumes linear relationships.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan
> wrote:
> > Hi Tsjerk
> >
> > Many thanks for your response. Do you think NMA
Hi Vijayan.R,
Not really. NMA also assumes linear relationships.
Cheers,
Tsjerk
On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan wrote:
> Hi Tsjerk
>
> Many thanks for your response. Do you think NMA is worth considering in such
> cases like this?
>
> Regards
> Vijayan.R
>
> On Thu, Dec 15,
Hi Tsjerk
Many thanks for your response. Do you think NMA is worth considering in
such cases like this?
Regards
Vijayan.R
On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar wrote:
> Hi Vijayan R.,
>
> > What i infer from this is that the cumulative variance experienced by
> the
> > top 10 P
Hi Vijayan R.,
> What i infer from this is that the cumulative variance experienced by the
> top 10 PC is hardly ~ 30 %.
Not experienced...; It's the variance captured by the first ten PC's.
> a) does this imply inadequate sampling by MD or a limited conformational
> change happening in the s
Dear GMXers,
I'm trying to manually add two sets of Urey-Bradley terms to the topology
file (in [angle] entry with type 5). However, it seems it is not allowed. I
got the following error:
Incorrect number of parameters - found 8, expected 4 or 4 for U-B.
Is it true that I can't do this in gromac
Hi all
I have a query about the eigenvalue values obtained from g_covar and
g_anaeig
I performed essential dynamics using PCA on my system (Protein-DNA
complex) considering BB of the protein and the phosphate and sugar of the
DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the
Thank you very much.
Best Regards
Sara
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Thursday, December 15, 2011 10:02 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
mohammad agha wrote:
> Thank you ve
mohammad agha wrote:
Thank you very much for your reply.
I experienced "genbox" for gromos force field for my molecules and for
dspc molecules in martini tutorial in lipid_tutorial.tar.gz, I took the
same warning for all them!!!
May I know that what should I do, Please ?
Probably nothing
mohammad agha wrote:
Dear Prof.
Thank you very much.
Excuse me, I am beginner in gromacs and my experience about warnings is
low, but I think my problem return to this warning:
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom names. Thes
Dear Prof.
Thank you very much.
Excuse me, I am beginner in gromacs and my experience about warnings is low,
but I think my problem return to this warning:
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom names. These numbers can deviate
thanks for your reply.
Best Regards
Sara
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Thursday, December 15, 2011 6:31 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
On 16/12/2011 1:36 AM, mohammad agha wro
Lina,
I used the same script for mpi ie other than usr/bin/poe I have given
usr/bin/mpirun I still receive the same errorOn 15/12/2011 4:51 PM, aiswarya pawar wrote:
>
> Hi,
>
>
> When i tried running mdrun without mip i received the same error ie
>
> when i gave mdrun -deffnm md
>
> i got=
> Bac
On 16/12/2011 1:36 AM, mohammad agha wrote:
Dear Prof.
Thank you for your reply.
I'm really sorry for my mistake in writing the density!! my calculated
density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
In the martini_v2.0.itp file, has been written "all particle masses
are
Dear Prof.
Thank you for your reply.
I'm really sorry for my mistake in writing the density!! my calculated density
become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
In the martini_v2.0.itp file, has been written "all particle masses are set to
72 amu". May I know my mistake, Pleas
Dear GRomacs users,
I am using the -rerun option of mdrun to read the coordinates of a trajectory
and to compute the potential energy of a molecule during MD.
This operation when performed in parallel, using mdrun_mpi, the energy of the
bonded interactions is not computed. But using one core,
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