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,
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
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
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
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
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
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
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
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
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
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 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
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,
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,
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
>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 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:
> > <
>
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
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 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 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
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
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 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
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
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