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.
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
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 luis.pinedadecas...@lnu.se
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
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
--
gmx-users mailing list
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 luis.pinedadecas...@lnu.se
I would first explain what do you mean
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
/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 luis.pinedadecas...@lnu.se
wrote:
So how would you
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 of the selected
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
trajectories from the same
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
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,
7, 2012 at 5:58 PM, Felipe Pineda, PhD
luis.pinedadecas...@lnu.se wrote:
ffamber.cnsm.csulb.edu/**amb2gmx.plhttp://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
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:
Hi again!
many thanks to Xavier
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 theoretical
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
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
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
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 OK?).
Many thanks in advance and best
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
--
gmx-users mailing listgmx-users@gromacs.org
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
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
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
, 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 pressure
coupling
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
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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