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,
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=
Back Off! I
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.
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 jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thursday, December 15, 2011 10:02 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
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
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
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 tsje...@gmail.com wrote:
Hi Vijayan R.,
What i infer from this is that the cumulative variance experienced by
the
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 biovija...@gmail.com wrote:
Hi Tsjerk
Many thanks for your response. Do you think NMA is worth considering in such
cases like this?
Regards
Vijayan.R
On
Thanks Tsjerk
On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar tsje...@gmail.com 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 biovija...@gmail.com
wrote:
Hi Tsjerk
Many thanks for your
Date: Thu, 15 Dec 2011 15:11:12 -0500
From: R.S.K.Vijayan biovija...@gmail.com
Subject: [gmx-users] Eigenvalue values from PCA (a general question)
To: gmx-users@gromacs.org
Message-ID:
camm9pawrymqrgzheriarvovk7qwuzpfwrm_owc_0+cemezm...@mail.gmail.com
Content-Type: text/plain;
Thanks Micheal for pointing out the mistake
On Fri, Dec 16, 2011 at 4:20 AM, Niesen, Michiel mnie...@coh.org wrote:
Date: Thu, 15 Dec 2011 15:11:12 -0500
From: R.S.K.Vijayan biovija...@gmail.com
Subject: [gmx-users] Eigenvalue values from PCA (a general question)
To: gmx-users@gromacs.org
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.
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
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
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 mnie...@coh.org wrote:
Date:
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
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
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 of a
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
24 matches
Mail list logo
