Dear Justin,
I am not sure to follow you. You essentially say that it is better to avoid
using implicit solvent i.e. the generalized Born-formalism implemented in
GROMACS?
For the case of optimizing and relaxing a system (expecting short MD), I agree
that it might be preferable to use
-0500
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Implicit solvent
On 2/14/13 10:21 AM, Sebastien Cote wrote:
Dear Justin,
I am not sure to follow you. You essentially say that it is better to avoid
using implicit solvent i.e. the generalized Born
Hello,
You might want to use TIPS3P (special CHARMM TIP3P) instead of regular TIP3P
because some researchers observed that regular TIP3P can impact the area per
lipid significantly when simulating CHARMM lipid bilayer (see reference below).
Concerning the CHARMM36 lipid force field in
Thanks a lot Mark!
Date: Wed, 15 Aug 2012 11:48:00 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Parameters for bonded interactions
On 15/08/2012 9:46 AM, Sebastien Cote wrote:
Dear Gromacs users
the .tpr file to 'human readable'?
Thanks again,
Sebastien
Date: Wed, 15 Aug 2012 11:48:00 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Parameters for bonded interactions
On 15/08/2012 9:46 AM, Sebastien Cote
Thanks Mark! This is exactly what I need.
Date: Wed, 15 Aug 2012 22:18:10 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Parameters for bonded interactions
On 15/08/2012 8:44 PM, Sebastien Cote wrote:
After
Thanks for the advices Chris.
My peptide is known to be more favorably to PE than PC membrane that is why I
am using POPE.
Experimentally, the liquid phase transition is at 298K for POPE (if I am not
mistaken). Is your 323K refer to some simulations?
At first I wanted to use the new
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
on here from
a couple of years ago).
On 012--8--9 2::4::9PPM -300,, Sebastien Cote wrote:
Dear Peter,
Did you use any different simulation conditions for your POPC membrane? I
tried many different ones for POPE, without never reproducing Klauda's
results. I may try yours on my POPE
not make a difference (although I switched to
h-bonds based on the suggestion of some charmm/lipid thread on here from
a couple of years ago).
On 2012-08-09 12:34:19PM -0300, Sebastien Cote wrote:
Dear Peter,
Did you use any different simulation conditions for your POPC membrane? I
tried
:28 AM, Sebastien Cote wrote:
Thanks for the suggestion. I tried it, but for my system the gain is not
significant.
I was aware that it is preferable to remove the centre-of-mass for each
leaflet separately. However, in my tests, I removed the center-of-mass of
the membrane
of the entire bilayer. This will allow the
system to equillibrate to the correct (higher) temperature, and should
increase the area per lipid of the bilayer.
Hope this helps.
-David
On Thu, Aug 2, 2012 at 8:22 AM, Sebastien Cote
sebastien.cot...@umontreal.ca wrote:
Dear Gromacs users,
I
for POPE - Why?
On 2012-07-23 02:34:31PM -0300, Sebastien Cote wrote:
There is not much difference when using DispCorr or not. At least on the
same time scale as the simulation with switch cutoff from 0.8 to 1.2 nm and
on the same time scale.
Should DispCorr be used in all membrane
,
Sebastien
Date: Fri, 20 Jul 2012 12:47:44 -0500
From: p...@uab.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
Did you play with DispCorr?
On 2012-07-20 09:46:13AM -0300, Sebastien Cote wrote
Dear Gromacs users,
My simulations on a POPE membrane using the CHARMM36 parameters are giving
''area per lipid'' values well below the experimental value (59.75-60.75
Angstroms2). Is their someone else experiencing a similar problem? If yes, how
did you solved it?
I did the following :
I
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