PME has a reciprocal component of the energy that cannot be calculated for each
individual atom. Hence it can't be assigned to an energy group (at least that
is my understanding).
I just use RF-0 to rerun the trajectory using a much larger cut off to try and
account for the errors that way. At
Thanks for that explanation.
I would like to know this with little more detail. What do you mean by RF-0
and which cut-off value are you talking about?
Rerunning the trajectory means the whole MD run again?
Thanks.
--
View this message in context:
Thanks for the advice, Mark!
I did exactly this experiment with the same expectations before posting
my query. I didn't get any complaint neither from grompp nor from mdrun,
what doesn't necessarily mean that this combination is implemented. I
just noticed that during equilibration results
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
number of coordinates in coordinate file (ctacyc.gro, 28794)
does not match topology (topol.top, 37950)
it means that I should enlarge the box to place all of solvent molecules into
that.
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
number of coordinates in coordinate file (ctacyc.gro, 28794)
does not match topology (topol.top, 37950)
it means that I should enlarge the box to place all of solvent molecules into
Hi Sara,
The number of molecules in your .gro file and .top file should be the same.
That means when you want to add 12000 solvent molecules, change the number of
solvent molecules in your topology file to 12000. The total number of your
solvent and solute molecules in you topology and
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,
Thanks for the reply. Then is any single trjconv command available before
viewing the trajectory file, or before extracting the xtc file, with that
command all the fraud caused by the PBC effect will be got rid of?
In addition, the box in the e-mail of Dr Dallas Warren should be the
Hi Emanuel,
Thank you very much from your response.
It means that it isn't one problem and it is natural.yes?
Best Regards
Sara
- Original Message -
From: Emanuel Birru emanuel.bi...@monash.edu
To: 'mohammad agha' mra...@yahoo.com; 'Discussion list for GROMACS users'
Hi Emanuel,
Thank you very much from your response.
yes, my topology is correct.
It means that it isn't one problem and it is natural.yes?
This question is because of in the most of papers has been said that the box is
enlarged with equilibrium but my box become smaller!
Best Regards
Sara
I am not sure whether a pressure coupling equilibration enlarges the specified
box size of the simulation :) if the box size is not appropriate to maintain
the pressure coupling the simulation probably blow up instead of adjusting the
box size to a bigger one.
For more info check the
On 14/08/2012 5:54 PM, Acoot Brett wrote:
Dear All,
Thanks for the reply. Then is any single trjconv command available before
viewing the trajectory file, or before extracting the xtc file, with that
command all the fraud caused by the PBC effect will be got rid of?
I linked a page with a
On 14/08/2012 5:27 PM, mohammad agha wrote:
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
What's it? genbox? grompp? You can't be helped effectively if you
don't provide your command lines that produce output, and/or a
description of
On 14/08/2012 6:16 PM, Emanuel Birru wrote:
I am not sure whether a pressure coupling equilibration enlarges the specified
box size of the simulation :)
It can.
if the box size is not appropriate to maintain the pressure coupling the
simulation probably blow up instead of adjusting the
Thank you very much.
Best Regards
Sara
- Original Message -
From: Emanuel Birru emanuel.bi...@monash.edu
To: 'mohammad agha' mra...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Cc:
Sent: Tuesday, August 14, 2012 12:46 PM
Subject: RE: [gmx-users] Fw: box of
Dear Mark,
Thank you very much from your help.
I used from genbox to place solvent molecules. my question is : In the NPT
ensemble, for equilibrium, may the box become smaller than definite sizes
before equilibrium(for example 2nm become smaller) and if yes, why haven't been
placed molecules
Dear All,
I wanted to ask that from where can I get the topologies and
co-ordinate information for Mg and K ions? For the ligands, I could
get it from PRODRG software as suggested in the tutorial but my
protein needs the crucial ions Mg and K before I can begin with my
simulations.
Best Wishes,
On 14/08/2012 6:55 PM, mohammad agha wrote:
Dear Mark,
Thank you very much from your help.
I used from genbox to place solvent molecules. my question is : In the NPT
ensemble, for equilibrium, may the box become smaller than definite sizes
before equilibrium(for example 2nm become smaller)
On 14/08/2012 7:45 PM, Ankita naithani wrote:
Dear All,
I wanted to ask that from where can I get the topologies and
co-ordinate information for Mg and K ions? For the ligands, I could
get it from PRODRG software as suggested in the tutorial but my
protein needs the crucial ions Mg and K before
Dear Mark,
Thank you for your reply.
I am using gromos53a6 force field.
On Tue, Aug 14, 2012 at 11:16 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/08/2012 7:45 PM, Ankita naithani wrote:
Dear All,
I wanted to ask that from where can I get the topologies and
co-ordinate
Dear Mark,
Thank you very much from your help.
Best Regards
Sara
- Original Message -
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Tuesday, August 14, 2012 2:44 PM
Subject: Re: [gmx-users] box of simulation
On
On 2012-08-14 14:27, tarak karmakar wrote:
Dear All,
In the manual I see the unit of the k{theta} is kJ/mol/rad^2. But
Neale et al in Chemical Physics Letters 460 (2008) 375–381 has applied
the harmonic restraints with a force constant of
0.0364 kcal/mol/deg^2 for the phi and psi dihedral angle
Thanks Mark for your reply. I was trying to use Single-Point Energy
Calculation as you advised in your first reply but for most of the
files the simulation failed because I was using the original .pdb
files in the mdrun command.
Anyways. I really appreciate your help.
Thanks again,
Jesmin
On
Hi Juliette ,
If your data is more and because of that may be -append not support you.
Then these may be help you ..
mdrun -v -deffnm use different name than previous -s your tpr file
-cpi cpt
See carefully the output and check the time at which the run
start..Is the starting time
Dear shima and Justin,
These error is come on Gromacs 4.5.5 at the time of NPT if
refcoord_scaling option not used..
But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling
option at npt
Is any one else has same experience?
I really surprised by my observation
With
On 8/14/12 11:15 AM, rama david wrote:
Dear shima and Justin,
These error is come on Gromacs 4.5.5 at the time of NPT if
refcoord_scaling option not used..
But it is not come on Gromacs 4.5.4 when you not use refcoord_scaling
option at npt
Is any one else has same experience?
I really
Justin,
Thank you for your reply,
I check the manual but it is giving only small information..
I would be greatly thankfull to you if you shed some light on
these option ...
With best wishes and regards
Rama David
--
gmx-users mailing listgmx-users@gromacs.org
On 8/14/12 11:28 AM, rama david wrote:
Justin,
Thank you for your reply,
I check the manual but it is giving only small information..
I would be greatly thankfull to you if you shed some light on
these option ...
A simple search of the list archive turns up lots of discussions like
Dear simulators,
we have a PhD position available in the Computational Molecular
Biophysics group in Göttingen (Germany). Please have a look here for
more details:
http://cmb.bio.uni-goettingen.de/jobs.html
Thank you,
Jochen
--
---
Dr. Jochen
Hi all,
I'm simulating a system of POPC and water for 50 ns. I set the job but it
interrupted in the middle of the job due to cluster problem and I got the
results up to 40 ns. Is it possible to continue it for the last 10 ns and not
doing the simulation from the beginning?
Please guide
On 8/14/12 1:49 PM, Shima Arasteh wrote:
Hi all,
I'm simulating a system of POPC and water for 50 ns. I set the job but it
interrupted in the middle of the job due to cluster problem and I got the
results up to 40 ns. Is it possible to continue it for the last 10 ns and not
doing the
Thanks for the link.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Tuesday, August 14, 2012 10:25 PM
Subject: Re: [gmx-users] simulation
On
Hi David,
Thanks for the reply. But I rechecked the paper [
http://www.sciencedirect.com/science/article/pii/S0009261408007975] as
I mentioned earlier, the unit of the harmonic force constant for the
dihedral is kcal/mol/deg^2. Again if the force constant unit is
independent of degree or radian
On 8/14/12 2:15 PM, tarak karmakar wrote:
Hi David,
Thanks for the reply. But I rechecked the paper [
http://www.sciencedirect.com/science/article/pii/S0009261408007975] as
I mentioned earlier, the unit of the harmonic force constant for the
dihedral is kcal/mol/deg^2. Again if the force
You are missing a major conceptual principle of MD here.
See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Read manual, section 3.2
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal
There are different methods used to calculate the electrostatics, RF-0 is one.
7.3.10 in the manual.
You can just use the -rerun flag in mdrun, after creating an appropriate .tpr
file with grompp and a new .mdp file.
If I understand it properly this effectively calculates single point
Dear Gromacs users,
In the topology file of the protein, we see every two atoms that share a bond,
three atoms that share a bond angle, and four atoms that share a torsion angle.
However, the parameters (equilibrium value, energy constant, phase) are not
explicitly shown as Gromacs fetch them
Dear Felipe,
I will take a lot at this paper.
Thanks!
Sebastien
Date: Tue, 4 Aug 012 9::8::7 +200
From: luis.pinedadecas...@lnu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] CHARMM6 - Smaller Area per lipid for POPE - Why?
Hi Sébastien,
Dear Peter,
I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm (as
in Klauda's paper). I will retry with a more solvated membrane.
Would you have any thought on how the NPAT ensemble might affect
peptide-membrane interactions like I am studying i.e. peptide is totally
On 15/08/2012 9:46 AM, Sebastien Cote wrote:
Dear Gromacs users,
In the topology file of the protein, we see every two atoms that share a bond,
three atoms that share a bond angle, and four atoms that share a torsion angle.
However, the parameters (equilibrium value, energy constant, phase)
Hi Justin ,
Thank you for immediate reply and providing the link.
But I am wonder for following things...
For protein simulation in your lysozyme tutorial we use
refcoord_scaling = com
In lipid tutorial also same one..
So Is there are any case when to use
refcoord_scaling no or all .??
On 15/08/2012 2:43 PM, rama david wrote:
Hi Justin ,
Thank you for immediate reply and providing the link.
But I am wonder for following things...
For protein simulation in your lysozyme tutorial we use
refcoord_scaling = com
In lipid tutorial also same one..
So Is there are any case when to
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