Hi,
Your data might have intrinsically strange time correlations,
but the chances are high that you have not sampled enough.
I would first also try the g_analyze of Gromacs 4.0, I have improved
some subtleties in the fitting weights there, which can help in certain
unstable cases.
But tau1 seems
Dear all
I want to do Hydrogen bond analysis for my MD data (protein-dna
interaction).
If anybody know the tutorial regarding that, please let me know.
Any help will highly appreciated!
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Please
On 02/02/10 16:50, PAVAN PAYGHAN wrote:
Thnx for replying
A]
As i hv mentioned previously that in my simulation g_rms suggests it
has some large peaks ,so applied trjconv with
-pbc nojump now ...
there are no peaks in rmsd its oky but in vmd it showed that water is
not having defined box so h
On 02/02/10 14:23, 011013021-Jyotsna wrote:
Dear David,
Thank you very much for your help.
As per the literature am following , it is mentioned that the bond
distance used is 0.7 Angstrom. Where do I incorporate the bond distance
parameter in the topology file?
See example in chapter 5 of the
Thnx for replying
A]
As i hv mentioned previously that in my simulation g_rms suggests it has
some large peaks ,so applied trjconv with
-pbc nojump now ...
there are no peaks in rmsd its oky but in vmd it showed that water is not
having defined box so how to tackle this situation..
1.which -
Dear David,
Thank you very much for your help.
As per the literature am following , it is mentioned that
the bond distance used is 0.7 Angstrom. Where do I
incorporate the bond distance parameter in the topology
file? The problem am facing is that , I am not very clear
as to if the distance i
rituraj purohit wrote:
Dear friends,
I want to do PCA for my MD data.
If anybody know the tutorial regarding PCA, please let me know.
Thanks in advanced
There's not so much a tutorial for PCA as there is a sequence of a few commands.
Tsjerk's lysozyme tutorial has an excellent section on P
ot;Justin A. Lemkul"
> Subject: Re: [gmx-users] tutorial for ionic liquid
> To: Discussion list for GROMACS users
> Message-ID: <4b66c6ab.2070...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Catarina Nunes wrote:
> > Dear all,
Dear Gromacs-Users,
I've been trying to figure out g_analyze for a while now (having read
the manual references and papers), but I still haven't found out what
a negative parameter obtained during fitting means. It's clear that
when Tau2 is longer than the total simulation time the sampling is
bad
On 2/1/10 4:32 PM, ms wrote:
Hi,
Sorry for the offtopic but Google/literature quick search is not helping
and I'd like to have some more informed opinion.
To my understanding, GROMACS isn't capable of discontinuous molecular
dynamics. Is there any more-or-less standard software package for that
Hi,
Sorry for the offtopic but Google/literature quick search is not helping
and I'd like to have some more informed opinion.
To my understanding, GROMACS isn't capable of discontinuous molecular
dynamics. Is there any more-or-less standard software package for that?
thank you!
m.
--
gmx-users
Hi,
This force field was designed to be used with constraints.
First try running with constraints set to all-bonds and without -DFLEXIBLE and
check
the densities again.
Berk
> Date: Mon, 1 Feb 2010 16:58:44 +0100
> From: ana...@fundp.ac.be
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re:
I have changed tau_t=0.2 for 1.0 but the density is not restored. I have tried
with the parameters from Villa and Mark (J Comput Chem, 2002, 23, 548)
, tau_t=0.2 and tau_p=2.0 and still get the same density. The self-diffusion
coefficient is indeed half of that with md with sd and tau_t=0.2 (0.7
On 02/02/10 01:29, ABEL Stephane 175950 wrote:
Hi GMXusers
I am testing the parameters of CHARMM, it works fine for lipids and protein. This
is a great job, thanks to the devellopers But i would like to add some new
molecule for solvent (e.g. for TFE) The atom types of TFE are present in the
Please keep GROMACS correspondence on the mailing list. Nobody here is a
private tutor unless you're paying them.
Original Message
Subject: Help for REMD
Date: Mon, 01 Feb 2010 14:58:08 +0200 (EET)
From: Murat Erman OGUZ
To: mark.abra...@anu.edu.au
Dear Mr.Mark Abraham
I am E
Hi GMXusers
I am testing the parameters of CHARMM, it works fine for lipids and protein.
This is a great job, thanks to the devellopers But i would like to add some new
molecule for solvent (e.g. for TFE) The atom types of TFE are present in the
ffcharmm27bon.itp available in latest port (c32b1
Thanks You all.
Mark you were right. Some how mpi was screwed up. Now I am able to run the
job parallely.
Actually there were two different versions of openmpi and I suppose they
were conflicting. Uninstalling both of them and instally the recent openmpi
solved the problem
Chandan
--
Chandan kuma
> Dear all,
> Do you have any tutorial for ?
> Best regards
> Catarina
I have worked with MD of RTILs quite a lot. So if you have got
concrete questions, you can probably ask me directly.
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
--
gmx-users mailing listgmx-users
S, I agree that MPI environment is to be configured,
this hostfile or the hosts can be defined in mpirun options.
mpirun --hostfile or mpirun --host
eg: mpirun –hostfile my_hostfile –np 4 a.out, mpirun –host
Host1,Host2,Host3,Host4 –np 4 a.out
mpi will use the hosts of this file Which can be us
oguz gurbulak wrote:
Dear All,
I'm searching for a non-equilibrium MD tutorial done with Gromacs.
Could you please help me to find a NEMD tutorial ?
"Non-equilibrium" can encompass a variety of topics, so if you want specific
advice, you'll have to be more specific. And, as I just men
Dear All,
I'm searching for a non-equilibrium MD tutorial done with Gromacs. Could you
please help me to find a NEMD tutorial ?
Thank in advance .
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at h
Catarina Nunes wrote:
Dear all,
Do you have any tutorial for ?
Best regards
Catarina
Gromacs tutorials can be found at:
http://www.gromacs.org/Documentation/Tutorials
If you don't find it there, try Google. If you don't find it there, it probably
doesn't exist :)
-Justin
--
===
Dear all,
Do you have any tutorial for ?
Best regards
Catarina
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use
On 2/1/10 10:57 AM, 011013021-Jyotsna wrote:
Dear all,
I want to run a simulation for an enzyme. It demands me to incorporate a
Molecular hydrogen Topology with a dummy atom in between in the
simulation in order to study the path of hydrogen in it.The problem is ,
the topology file I built induc
Dear all,
I want to run a simulation for an enzyme. It demands me to
incorporate a Molecular hydrogen Topology with a dummy
atom in between in the simulation in order to study the
path of hydrogen in it.The problem is , the topology file
I built induces many errors when i come to the energy
On 01/02/10 21:41, bharat gupta wrote:
hi all,
Can anyboddy tell me from where I can get full detail of MPI with
respect to GROMACS ..
This question is too general. Please search the GROMACS website for
whatever you're really searching for, and if that fails, ask a focussed
question.
Mark
-
On 01/02/10 20:19, Sarath Kumar wrote:
Message: 2
Date: Mon, 1 Feb 2010 12:31:32 +0530
From: Chandan Choudhury mailto:iitd...@gmail.com>>
Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
mpicc
To: Discussion list for GROMACS users mailto:gmx-
hi all,
Can anyboddy tell me from where I can get full detail of MPI with
respect to GROMACS ..
--
Bharat
M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Puducherry
India
Mob. +919962670525
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http://lists.gromacs
gmx-users-requ...@gromacs.org wrote:
Thanks for the info Mark.
Dear All
Some time ago there was a discussion concerning the problems of REMD for
large systems and the possibility of using the REST implementation of
the method.
Mark, you mentioned that you had coded an implementation Okur method
Message: 2
> Date: Mon, 1 Feb 2010 12:31:32 +0530
> From: Chandan Choudhury
> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
>mpicc
> To: Discussion list for GROMACS users
> Message-ID:
><4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com>
> Content
On 01/02/10 18:50, David van der Spoel wrote:
On 2/1/10 6:01 AM, Mark Abraham wrote:
On 27/01/10 19:00, David Parcej wrote:
Dear All
Some time ago there was a discussion concerning the problems of REMD for
large systems and the possibility of using the REST implementation of
the method.
Mark, y
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