On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Gmx Users,
I would like to calculate the interaction energy (LJ and electrostatic)
between each residue and my ligands (10 ligands in the system). I would like
to see what is the
On 2011-10-17 22:58, Justin A. Lemkul wrote:
Yao Yao wrote:
Hi Gmxers,
Is there a way I can check all the kinds of solvents in gromacs? Apart
from water, ethanol, ...,
are there any Glycerol, Treholose,
There likely aren't many. Anything available would be in the force field
Dear Justin,
Indeed I didnt take into account square degree so all values presented in
the tutorial exactly true so this was exactly my mistake. :(
After some iterations I've obtained value for S per lipid beetween 0.65-0.71
A^2. This is the example of the system wich I've obtained after
I have been performing MD simulation on electrolyte solution recently. And I
want to calculate the dipoles between cation-anion pairs. But I have no clue
how to achieve this by gromacs. I also want to know the algorithm for command
g_dipole about how to cheat a system with both molecules and
Hello,
Thank you. I got the point but I have a doubt,
equilibrate under NPT until the pressure and
temperature are stable, then switch to NVT to
eliminate the boiling issue, how exactly it will
eliminate the boiling issue if we dont use higher
pressure while equlibrating? (as you said that
it is
Dear Gromacs users,I would like to ask how I could vizualise the violations of the dihedral restraints in detail, i.e., a list of all violations.As far as I know, there is nothing like g_disre for dihedrals, or ?Kind regardsMarkusSMS schreiben mit WEB.DE FreeMail - einfach, schnell
Steven Neumann wrote:
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Gmx Users,
I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my
James Starlight wrote:
Dear Justin,
Indeed I didnt take into account square degree so all values presented
in the tutorial exactly true so this was exactly my mistake. :(
After some iterations I've obtained value for S per lipid beetween
0.65-0.71 A^2. This is the example of the system
Kavyashree M wrote:
Hello,
Thank you. I got the point but I have a doubt,
equilibrate under NPT until the pressure and
temperature are stable, then switch to NVT to
eliminate the boiling issue, how exactly it will
eliminate the boiling issue if we dont use higher
pressure while equlibrating?
On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Gmx Users,
I would like to calculate the
Ok Thanks.
On Tue, Oct 18, 2011 at 4:41 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Hello,
Thank you. I got the point but I have a doubt,
equilibrate under NPT until the pressure and
temperature are stable, then switch to NVT to
eliminate the boiling issue, how
Steven Neumann wrote:
On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu
Message: 1
Date: Tue, 18 Oct 2011 06:41:55 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Interaction energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4e9d57f3.10...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Steven
On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
Message: 1
Date: Tue, 18 Oct 2011 06:41:55 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Interaction energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
Steven Neumann wrote:
On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs lloyd.ri...@gmx.ch
mailto:lloyd.ri...@gmx.ch wrote:
Message: 1
Date: Tue, 18 Oct 2011 06:41:55 -0400
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] Interaction energy
hey guys,
i'm a really confused at the moment. reading the gromacs manual 4.5.4
(GM) and the paper introducing GAFF did not provide insight into this
issue which drives me crazy! maybe some advanced gromacs user can do so.
up to now, i have simulated very few different systems using amber
Hello,
I am new to gromacs. I am applying the pdb2gmx tool to a peptide that
has an N-term pyroglutamate and a C-term amidation. The OPLS
forcefield has an entry for PGLU.
I used the -ter flag of pdb2gmx to define protonation states of the
termini. While this works fine for the C-term
On 19/10/2011 12:34 AM, Vedat Durmaz wrote:
hey guys,
i'm a really confused at the moment. reading the gromacs manual 4.5.4
(GM) and the paper introducing GAFF did not provide insight into this
issue which drives me crazy! maybe some advanced gromacs user can do so.
up to now, i have
On Tue, Oct 18, 2011 at 2:50 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Tue, Oct 18, 2011 at 1:36 PM, lloyd riggs lloyd.ri...@gmx.ch mailto:
lloyd.ri...@gmx.ch wrote:
Message: 1
Date: Tue, 18 Oct 2011 06:41:55 -0400
From: Justin A. Lemkul
Dear Gromacs user . Thanks for your previous eply
I am using plumed gromacs . i would like to
find out Hydrophobic interaction free energies . As stated in manual.i used
COORD keyword which is based on the Switching function . But When i use the
COORD
On 17.10.2011 05:18, Mark Abraham wrote:
On 17/10/2011 7:04 AM, Mirco Wahab wrote:
On 10/16/2011 2:25 PM, Mark Abraham wrote:
On 15/10/2011 9:02 PM, Mirco Wahab wrote:
On 10/15/2011 1:15 AM, Mark Abraham wrote:
I use
...
...
...
OK, I can understand that. But if the options (-mtune ***,
Dear users,
Sometimes, in the end ( in production simulation), Gromacs doesn't show
calculation/finish time on screen, why? How can we show it?
Thanks in advance
--
Ahmet YILDIRIM
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please
Greetings!
Recently I've found that Charmm27 ff is widely used for the simulation of
the membrane proteins. I've tried to work with pure DPPC bilayer in pdb2grx
and obtain that charm27 ff included in the Gromacs is lack for the
parametries for the lipids.
Could you tell me where I could obtain
James Starlight wrote:
Greetings!
Recently I've found that Charmm27 ff is widely used for the simulation
of the membrane proteins. I've tried to work with pure DPPC bilayer in
pdb2grx and obtain that charm27 ff included in the Gromacs is lack for
the parametries for the lipids.
Could
By default in the CHARMM27 force field files there is no DPPC, as this
is made up from a combination of other entries in the rtp file (because
this is the way it is done in the CHARMM program's files). If you wish
to use DPPC you can construct yourself a complete DPPC rtp entry. To do
this you
I posted to the list a few days ago with an energy drift problem.
Mark Abraham helpfully suggested using all-bonds rather than h-bonds
which solved the problem. I'm now trying to understand quite why that
helped so much.
The simulation is a protein of about 5000 atoms using GBSA, a time
step of
Ben Reynwar wrote:
I posted to the list a few days ago with an energy drift problem.
Mark Abraham helpfully suggested using all-bonds rather than h-bonds
which solved the problem. I'm now trying to understand quite why that
helped so much.
The simulation is a protein of about 5000 atoms
Dear All,
I have a simulation set up for a mixture of carbon dioxide and water system
which runs perfectly on Gromacs 4.0.5 version. I have run these simulations
at different temperatures and pressures, from the same starting
configuration and the simulation proceeds smoothly in the 4.0.5
Dear justin,
Thanks for your replies.
i am doing Steered MD .. i would like to
calculate radial Distribution function. of Moving group with respect to
Fixed group . I am pulling only in Z direction then is it possible to
calculate
HiSapna,I had the same problem few weeks ago.Apparently, some parameters are different (eg.nstpcouple).Cheers,ItamarPSI found out that I prefer to stick to 4.0.7.---BeginMessage---
That seems possible Mark. I had actually assumed that Itamar extracted
a .gro from the 4.0.7 simulations and
vidhya sankar wrote:
Dear justin,
Thanks for your replies.
i am doing Steered MD .. i would like
to calculate radial Distribution function. of Moving group with
respect to Fixed group . I am pulling only in Z direction then is it
Dear justin,
Thanks for you Immediate reply but When i surf the
following site
http://www.linux-support.com/cms/en/component/content/article/12-man-pages/31116-g-rdf-calculates-radial-distribution-functions-man1
I got he following information
g_rdf calculates radial
Dear Itamar,
Thank you for your response. Why did you prefer to stick to 4.0.7? Is there
something particularly difficult to transfer from 4.0.7 version to 4.5
version?
Sapna
On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass itamar.k...@monash.edu wrote:
Hi Sapna,
I had the same problem few
vidhya sankar wrote:
Dear justin,
Thanks for you Immediate reply but When i surf the
following site
http://www.linux-support.com/cms/en/component/content/article/12-man-pages/31116-g-rdf-calculates-radial-distribution-functions-man1
I got he following information
g_rdf
Hi Sapna,
It is a good question, but such of personal preferences. I found out that my
simulations tend to crash more often when I am using 4.5.5. It might be the
General-reaction -field I use or something else, I am not sure. Also, it seems
I will not gain much from upgrading, so I stick to
Itamar Kass wrote:
Hi Sapna,
It is a good question, but such of personal preferences. I found out
that my simulations tend to crash more often when I am using 4.5.5. It
might be the General-reaction -field I use or something else, I am not
sure. Also, it seems I will not gain much from
Dear all,
I would like to do MD simulations of polymer binding to lipid bilayers.
To that end I have generated the following components:
- CgenFF-based force field for the polymers' monomeric units (tested
in NAMD/CHARMM)
- CHARMM36 lipid force field for the lipid bilayers with some added
On 19/10/2011 5:26 AM, ahmet yıldırım wrote:
Dear users,
Sometimes, in the end ( in production simulation), Gromacs doesn't
show calculation/finish time on screen, why? How can we show it?
I don't know what you mean.
Mark
--
gmx-users mailing listgmx-users@gromacs.org
You can get them in the log file. (At the bottom)
Cheers,
=
Emanuel Birru
PhD Candidate
Faculty of Pharmacy and Pharmaceutical Sciences
Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia
Tel:
Dear gmx-users,
Does anyone know where can I find any explanations about the atom names in
ffbonded.itp file in oplsaa.ff? I am trying to compare the amino acids'
parameters in gromacs 4.5.4 with in tinker. Or where to find the default
parameters gromacs takes for amino acids in its
On 19/10/2011 3:50 PM, mu xiaojia wrote:
Dear gmx-users,
Does anyone know where can I find any explanations about the atom
names in ffbonded.itp file in oplsaa.ff? I am trying to compare the
amino acids' parameters in gromacs 4.5.4 with in tinker. Or where to
find the default parameters
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