https://mcule.com/apps/1-click-docking/
On 03/01/2013 11:03 AM, James Starlight wrote:
Dear Gromacs Users!
During preparation of the protein-ligand complex (manual placement of
the ligand into the ligand-binding pocket (based onto known x-ray
data) I've forced with the overlap of some polar si
If all atoms belonging to one chain are put together in a group, then
the xvg files are empty.
There should be some posting in the archive clarifying the issue, but
was not able to find it yet.
Thanks,
Felipe
On 02/20/2013 04:17 PM, Justin Lemkul wrote:
On 2/20/13 9:41 AM, Felipe Pineda, P
Hi,
is it possible to apply g_order to a trajectory of a lipid bilayer when
the carbon atoms of the acyl chains of the lipid molecules for which the
SCD should be calculated are not numbered consecutively, i.e. the atom
numbers corresponding to C21-C22-C23-... (sn-2 chain) are eg 23 22
1
Have you maybe tried this?
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List/Search?q=%22vacuum+simulation%22
Own initiative and discrete thinking is mandatory for research.
On 02/19/2013 12:32 PM, raji wrote:
for vacuum simulation , no need to specify cut-offs right. am using 8x8x8
Thank the documentation, which you should probably read more carefully
the next time. Reading comprehension and discrete thinking are key.
On 02/14/2013 10:59 AM, James Starlight wrote:
Felipe,
thats works perfect! thank you!
James
2013/2/14 Felipe Pineda, PhD :
It's all
It's all about comprehending reading. If you look carefully at the
documentation again, you will find:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
What it's the right thing to do.
On 02/14/2013 10:11 AM, James Starlight wrote:
I've already tr
Very frequently it helps just to do some searches by your own and read
_carefully_ the documentation:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend
On 02/14/2013 08:13 AM, James Starlight wrote:
Dear Gromacs Users!
I have completed 100ns md trajectory.
I
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
On 01/21/2013 11:20 AM, Kieu Thu Nguyen wrote:
Dear All,
I intend to run a long-time MD process. Can i split it into many smaller
processes without losing system properties ? Is that the following process
will be followed from t
changed
the activation energy.
You would probably need some kind of (ab-initio) QM calculation to study
this. It would be a better idea to ask, e.g., the Gaussian community (in
CCL) for advice.
2013/1/14 Felipe Pineda, PhD
I would first explain what do you mean with activation energy. What
I would first explain what do you mean with activation energy. What
definition do you use?
On 01/14/2013 01:15 PM, Ahmet yıldırım wrote:
Dear users,
Is it possible to calculate the activation energy of a structure using
Gromacs? if OK, how?
Thanks in advance
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gmx-users mailing listgmx-
Maybe you can try first another tutorials, eg.
http://manuals.bioinformatics.ucr.edu/home/linux-basics
On 01/03/2013 03:16 PM, amna khan wrote:
the command
/usr/share/gromacs/tutor/gmxdemo/demo
no such cooamnd found...
cd /usr/share/gromacs/tutor/gmxdemo/demo
permsion denied
sudo /usr/shar
ng it takes for such differences to really
manifest.
Best,
Erik
22 nov 2012 kl. 10.13 skrev Felipe Pineda, PhD:
Would "non-deterministic" be correct to characterize the nature of MD as well?
There is also deterministic chaos ... And what about the outcome of starting several
trajec
kl. 09.52 skrev Felipe Pineda, PhD:
Won't this same stochastic nature of MD provide for different, independent
trajectories even if restarted from a previous, equilibrated frame even without
resetting velocities, i.e., as a continuation run using the velocities recorded
in the gro file
11/22/2012 12:55 AM, Mark Abraham wrote:
Generating velocities from a new random seed is normally regarded as good
enough. By the time you equilibrate, the chaotic nature of MD starts to
work for you.
Mark
On Nov 21, 2012 1:04 PM, "Felipe Pineda, PhD"
wrote:
So how would you repeat
So how would you repeat the (let be it converged) simulation from
different starting conditions in order to add that valuable statistics
you mention?
I think this was Albert's question
Felipe
On 11/21/2012 12:41 PM, Mark Abraham wrote:
If a simulation ensemble doesn't converge reliably over
7, 2012 at 5:58 PM, Felipe Pineda, PhD <
luis.pinedadecas...@lnu.se> wrote:
ffamber.cnsm.csulb.edu/**amb2gmx.pl<http://ffamber.cnsm.csulb.edu/amb2gmx.pl>
On 11/07/2012 09:45 AM, Rajiv Gandhi wrote:
Dear Gromacs user,
I have found the parameters file for my ligand which is availa
ffamber.cnsm.csulb.edu/amb2gmx.pl
On 11/07/2012 09:45 AM, Rajiv Gandhi wrote:
Dear Gromacs user,
I have found the parameters file for my ligand which is available in AMBER
distribution parameter database, Could you advice me how do i use them in
running over MD in gromacs? Thanks in advance,
artifacts in charged periodic systems via net charge corrections to the
ewald potential. Journal of Chemical Physics. 1998;108(17):7070-84.
<http://jcp.aip.org/jcpsa6/v108/i17/p7070_s1>).
Felipe
On 11/05/2012 02:27 PM, Justin Lemkul wrote:
On 11/5/12 8:16 AM, Felipe Pineda, PhD wrote:
are not correct when the system is not neutral. In your case the
charge is significantly high ...
On Nov 2, 2012, at 9:36 AM, Felipe Pineda, PhD wrote:
Hi,
I recently sent a query, but it was probably not appealing enough to
get some feedback. So I try again with a shorter one:
Is there any
Hi,
I recently sent a query, but it was probably not appealing enough to get
some feedback. So I try again with a shorter one:
Is there any theoretical or technical objection against running an
NPgammaT simulation on a charged (total charge = -36) membrane model
(hydrated bipolar monolayer)
Dear Colleagues,
I am currently carrying out MD simulations on models of archaeal
membranes. These membranes, contrary to those of bacteria or eukariota,
are made of unconventional lipids. In my case they contain a neutral
carbohydrate headgroup and the second one is a negatively charged
phos
Hi,
packmol generates just coordinates (pdb format) for optimized packing
arrangements of whatever molecule you provide as input. It's up to you
to parameterize the resulting model. CHARMM-GUI has a library of
conventional (phospho)lipids and generates the input for CHARMM
equilibration of th
To generate starting (non-equilibrated) bilayer structures for use in MD
simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/.
Otherwise, for conventional lipids CHARMM-GUI membrane builder
(http://www.charmm-gui.org/?doc=input/membrane).
Hope it helps!
Felipe
On 10/04/201
ny thanks again in advance and kind regards,
Felipe
On 09/27/2012 03:49 PM, Felipe Pineda, PhD wrote:
Hi,
I'd greatly appreciate any general advice on the possibility to use
several (2 or more) tc_grps with v-rescale and how large could be
tau_t with this coupling method (is 0.3 ps still
Hi,
I'd greatly appreciate any general advice on the possibility to use
several (2 or more) tc_grps with v-rescale and how large could be tau_t
with this coupling method (is 0.3 ps still OK?).
Many thanks in advance and best regards,
Felipe
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gmx-users mailing listgmx-users@gromacs.org
On 09/25/2012 10:08 AM, naga sundar wrote:
Dear Felipe
Thanks for ur reply.
The system is a protein-protein complex. Like u r saying its due
to pbc problem then why any abnormality doesn't happened to the native
complex (Black line)?.
Maybe because MD is stochastic
It looks for me like the known pbc effect others already pointed to. If
you have just a protein-ligand complex (+ water and counterions of
course) it's relatively easy to manually (a piece of code would do it)
bring the ligand to the correct position in the frames showing an
abnormally high val
Hi Sébastian,
I think the "magic word" in this issue would be surface tension and the
proper ensemble for the simulation NPgammaT. This is very well discussed
in the paper I advised to you a couple of days ago. The issue is by no
means trivial, although I'm not an expert to judge it. You can f
Hi Sébastien,
I found the following paper very instructive about this issue (simulated
areas per lipid in bilayers):
Jensen, M. et al. Simulations of a membrane anchored peptide: structure,
dynamics, and influence on bilayer properties. Biophys. J. (2004)86, 3556-75
Take maybe a look at it,
2 07:28 AM, Mark Abraham wrote:
On 13/08/2012 7:21 PM, Felipe Pineda, PhD wrote:
Dear All,
the Gromacs User Manual V.4.5.4 states on p. 33: "(...) the surface
tension and the z-component of the pressure can be coupled to a
pressure bath. Presently, this only works with the Berendsen pr
Dear All,
the Gromacs User Manual V.4.5.4 states on p. 33: "(...) the surface
tension and the z-component of the pressure can be coupled to a pressure
bath. Presently, this only works with the Berendsen pressure coupling
algorithm in GROMACS."
My question: does this hold for V. 4.5.5 as well
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