Hi Kevin,
Thanks.
Houyang
On Thu, Oct 24, 2013 at 3:00 PM, sri2201 wrote:
> Hi
> I would like to try it out
>
> Srinivasa Rao Penumutchu
> Research Scholar
> Protein NMR Lab , II floor-218
> Department of Chemistry
> National Tsing Hua University,
> Hsinchu, Taiwan.
> Ph: 886357151-35605,
> Emai
Hi Kevin
Can I have a try?
Best
Houyang
On Wed, Oct 23, 2013 at 12:30 PM, Villarealed wrote:
> Sound nice. I would like to try out.
> Could You please set up an account for me?
> Regards,
> Eduardo Villarreal
> villarea...@hss.edu
>
> -
> Eduardo Villarreal Ramírez
> Postdoctoral Research F
There shouldn't be a problem for that. BTW, can you also enter a ticket at
Daigrid.org for this matter?
Thanks
-Kevin
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of rajat desikan
Sent: Wednesday, October 23, 2013 1:24 AM
To: Di
Hi Michael,
Sorry, if this is not the right place to post message of such. To answer
your question, it is a web-based GUI interface to GROMACS, which is a
perfect fit for those who are trying to learn MD or to run large scale
protein simulations on HPC.
Best Regards,
Kevin"Feng"
icipate in user
testing on this newly developed tool. Let me know if you'd like to try it
out. We will set up an account for you.
Best Regards,
Kevin Chen, Ph.D.
Information Technology at Purdue (ITaP)
West Lafayette, IN 47907-2108
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gmx-users mailing listgmx-users@gromacs.org
http
t; --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search
I think you should add -tau 0 when using flooding as harmonic restraint
(since you do not want the flooding potential to change).
Okay, adding -tau 0 does turn it properly into a harmonic potential,
according to edsam.xvg. However, the average position of the resulting
(gaussian) is near but not
Hi all,
I can't seem to find the correct combination of EDI parameters impose a
harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2, and
I'd like to confirm that the inputs I have are actually correct. Here is the
make_edi command I used to generate the .edi file fed to m
; file. Is it still under
development?
2013/5/24 Erik Marklund
> Hm. That is peculiar. The source code has the answer of course. I can have
> a look next week to see why that is.
>
> Erik
>
> On 24 May 2013, at 14:11, CHEN Pan wrote:
>
> > Hi,
> >
> > I have 51
the summation of population is 200.
2013/5/24 Erik Marklund
> Hi,
>
> See below
>
> On 24 May 2013, at 11:45, CHEN Pan wrote:
>
> > Dear Gromacs users,
> >
> > I am confused about the g_hbond tools.
> >
> > 1) When I use "-dist" to ge
Dear Gromacs users,
I am confused about the g_hbond tools.
1) When I use "-dist" to get the distribution of hydrogen bonding distance,
I found that the summation of the population is always 200 (the y-column
below). I am not sure if it's was done with normalization or not, if yes,
the summation s
Hi Maggin,
The middle column is the total number of hydrogen bonds in your system
under the definition of the hydrogen bonds criteria you have defined (here
you used the default value). The third column is the number of
acceptor-donor paris in the system. The first column is the simulation
time, yo
much
Wayne Chen
--
View this message in context:
http://gromacs.5086.n6.nabble.com/How-to-maintain-the-same-exact-positions-of-the-protein-and-ligand-in-the-extracted-frame-pdb-file-a-tp4998045.html
Sent from the GROMACS Users
Hi,
I would like to calculate the nematic order parameter of organic liquid
crystals.
Is it possible to use the 'g_order' command in gromacs to do that? Or do I need
to write my own script? Or are there softwares/scripts out there that can
already do the job?
Thanks,
Serene
This email and an
, is there a problem to restart simulations from trrr file? And
how to restart from cpt file, solving that Segmentation Fault? Could someone
give me help on this? Thanks
chen
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Please searc
:
>Chen,
>
>to answer this, please see David's post and my reply. To answer if
>your unfolded state ensemble is accurate, you will need to know some
>experimentally evaluated quantities of the state that you are trying
>to reproduce: 498K, 26 atm, a certain amount
>At 2010-10-18 16:38:30，"David van der Spoel" wrote:
>>On 2010-10-18 06.56, chris.ne...@utoronto.ca wrote:
>> Generally, forcefields are not parameterized for temperatures other than
>> 298K, so simulations are not expected to reproduce the expected
>> properties (like boiling water and the corr
>At 2010-10-18 12:56:31，chris.ne...@utoronto.ca wrote:
>Generally, forcefields are not parameterized for temperatures other
>than 298K, so simulations are not expected to reproduce the expected
>properties (like boiling water and the correct temperature
>denaturation of proteins).
>
>There'
Hi All,
I met a problem when I try to unfold a protein using Gromacs, It seemed the
protein cannot be totally unfolded!
The simulated system has one Engrailed Homeodomain (En) protein (a three helix
bundle protein with 54 residues, 629 atoms), total 4848 spce waters, and 7 Cl-
used to neutrali
Hi gromacs user,
We recently ran in this problem when try to analyise our REMD
trajectories. g_kinetics module will be used for such kinda analysis,
however it looks like we need provide 2 xvgs file as input. The temp.xvg we
can get from demux.pl and the other one (data.xvg) we are not sure how
r attention to, but my point is
that this should always be done with great care, since small inaccuracies
in transplanting ion parameters can have dramatically bad results due to the
large energies involved (see Cheatham & Young's original report or my own in
http://pubs.acs.org/doi/abs/10.
h I do not have any experience using these
parameters.
Hope it helps your aggregation problems!
Alan Chen
> Date: Mon, 1 Jun 2009 14:52:35 -0300
> Subject: RE: [gmx-users] crystals of KCl during simulation
> From: mo...@ufscar.br
> To: gmx-users@gromacs.org
>
> Hi
Dear all,
Recently,We have tried to implement our own version of frce felds into
Gromacs 3.3.3. On the purpose of testing, we dumped out all the infrmation from
tpr by using gmxdump. Everything goes fine except this 1-4 interactions terms.
The prblem we had is that even though we had set numb
For example, I want to add GTP as residue current force field, and after
that pdb2gmx will be able to recognize GTP molecule.
At first, I created GTP.pdb:
REMARK This PDB file is created by CS Chem3D
REMARK
COMPND Untitled-1.pdb
HETATM1 C UNK 0 -0.561 0.002 -1.145
C
H
Dear Gromacs Users,
I am wondering if a QM/MM interface between Gromacs and Gamess-US has
already been available, or it will be available in the upcoming
Gromacs_4? I know that Gromacs_3 has an interface for Gamess-UK, which
is unfortunately not free for users outside UK.
Thanks.
Hanning
Hi Cong:
To expand on Mark's answer, there is no "universal test" for convergence
of all properties, and therefore the best you can ever hope to do is
check for convergence of the observable(s) you care
about, and any closely related quantities you can think of (especially,
as previously menti
abouts?
Thanks,
Alan Chen
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run lots of independent trajectories of medium
(~100,000 atom) sized systems in our lab.
If anyone can share their experiences with gromacs on clovertown XEON
systems it would be greatly appreciated!
Thanks!
Alan Chen
graduate student - Pappu Lab
Center for Computational Biology
Washington Univ
This often happens if the sodium ion is not called "NA+" in the
forcefield
you have invoked. It might be "NA" or "Na+" - look at
ions.itp and see what the
correct name for the sodium ion is for the force field you are choosing
and
make sure it exactly matches the name you used in the topology
fi
) you
would find at the same concentration . . .
Cheers!
Alan Chen
Graduate Student
Pappu Lab
Washington University in St. Louis
Erik and all,
> No, I don't think so, or at least it's not our typo :-)
>
> It is quite common that ions end up with strange radii when you
> paramet
Hi,
For the past few days , we've been carrying out a simluation by using PPPM ,
for some reason we end up with some wired pressure tensors. Based on manual ,
it says it is not easy to calculate the full long-range virial tensor with PPPM
correctly, but it is possible to obtain the trace. Wha
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