On 18/05/2012 2:52 AM, francesco oteri wrote:
Dear gromacs users,
I am trying to port a set of charm parameter in gromacs.
I am using the script convert_charmm_to_gromacs.pl
http://convert_charmm_to_gromacs.pl contained in the
file charmm_to_gromacs.tgz
On 17/05/2012 11:48 AM, kevin wrote:
Thanks. I think I should have a look at some specific documents
to understand the flow of control.
Namely, to understand what is purpose of the subroutines
in src/mdlib/. But I could not find such
information in the Gromacs user manual. Do anyone know
On 17/05/2012 11:47 PM, Lara Bunte wrote:
Hello
After
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
I got the error:
Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
I thought that this could be an inconsistency be declaring the functions, but
in my topology
Dear all,
While i am running gromacs software i am getting following
error.Let me know how to over come that error
Fatal error:
number of coordinates in coordinate file (208L_ion.gro, 62283)
does not match topology (208L.top, 62293)
Suryanarayana Seera,
PhD student,
On 18/05/2012 4:43 PM, Seera Suryanarayana wrote:
Dear all,
While i am running gromacs software i am getting following
error.Let me know how to over come that error
Fatal error:
number of coordinates in coordinate file (208L_ion.gro, 62283)
does not match topology
Dear all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.
Fatal error:
Residue 'CSD' not found in residue topology database
Suryanarayana Seera,
PhD student,
Hyderabad,
India.
--
gmx-users mailing list
On Fri, May 18, 2012 at 12:20 PM, Seera Suryanarayana
paluso...@gmail.comwrote:
Dear all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.
Fatal error:
Residue 'CSD' not found in residue topology database
First read:
On 18/05/2012 4:50 PM, Seera Suryanarayana wrote:
Dear all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.
Fatal error:
Residue 'CSD' not found in residue topology database
Please search for your own answers before
On 18/05/2012 6:14 AM, mohan maruthi sena wrote:
Hi all,
I have used a user define potential to describe attractive
potential beyond i and i+3 atoms(similar to lLJ). If i want to
describe repulsive interactions with in i and i+3 , how can i do it in
gromacs? can anyone suggest me a
Hi
I have two questions left:
1.)
You wrote
If your term in question is an angle potential, then the force constant should
indeed have units of energy
Could you please explain this? Why is it here consistent to have Energy as unit
for a force constant?
2.)
The force constant is divided
Hi Chris,
I understand your question, this autocorrelation time puzzled me for a
long time as well. Not far from the interpretation you give, Scott
Feller defines it (http://dx.doi.org/10.1007/978-1-59745-519-0_7) as the
time a given observable takes to lose the memory of its previous state,
On Fri, May 18, 2012 at 12:30 AM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/17/12 4:45 PM, Steven Neumann wrote:
On Thu, May 17, 2012 at 5:48 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
On 5/17/12 11:50 AM, Steven Neumann wrote:
My tube is finite.
On Fri, 2012-05-18 at 09:40 +0100, Lara Bunte wrote:
Hi
I have two questions left:
1.)
You wrote
If your term in question is an angle potential, then the force constant
should indeed have units of energy
Could you please explain this? Why is it here consistent to have Energy
Hi,
at the link http://dl.dropbox.com/u/40545409/charmm2itp.tgz you can find
the files I am using
Files ffcharmmnb.itp ffcharmmbon.itp have been generated through:
convert_charmm_to_gromacs.pl par_all36_carb.prm
while carbohydrates.rtp and carbohydrates.rtp through a script of mine.
Now, if
That helps a lot. Thank you, I guess I got it now :-)
Greetings
Lara
- Ursprüngliche Message -
Von: Richard Broadbent richard.broadben...@imperial.ac.uk
An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users
gmx-users@gromacs.org
CC: jalem...@vt.edu jalem...@vt.edu
On 5/18/12 6:58 AM, Steven Neumann wrote:
Dear Gmx Users,
My system consists of a Tube made of Oxygen, Hydrogen and ions. These atoms are
not connected via bonds. I try tu run EM:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and
Hi Patrick,
Your response is indeed more useful that my previous answer and with
interesting links
thank for the pointers
Stephane
--
Message: 4
Date: Fri, 18 May 2012 10:51:35 +0200
From: Patrick Fuchs patrick.fu...@univ-paris-diderot.fr
Subject: Re:
Hi Steven
You've tried with constraints = none, but that still keeps constraints
over water molecules through SETTLE algorithm. Maybe you can try a
minimization with define = -DFLEXIBLE to remove settle over water and
then try again a constraint (settle) minimization.
Javier
El 18/05/12
According to the roadmap that you mentioned, the first thing to do is to
change a little bit some parts of the g03 code, and reinstalling it from
this new source. So, you can do it only if your g03 license includes
access to the source code.
If not, you can try other QM packages, such as
On Fri, May 18, 2012 at 12:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:
I have no idea why you observe the dip, but it's probably irrelevant as
you don't need a reaction coordinate that long, if this is the same plot
that we've been discussing on the list.
I must ask that you always post
On Fri, May 18, 2012 at 12:20 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/18/12 6:58 AM, Steven Neumann wrote:
Dear Gmx Users,
My system consists of a Tube made of Oxygen, Hydrogen and ions. These
atoms are
not connected via bonds. I try tu run EM:
; minim.mdp - used as input into
Dear gmx users,
Imagine it's a protein-membrane system which GROMOS53a6 and CHARMM36 will give
me the same acceptable output for a protein-membrane system. Now if I want to
choose one, what am I supposed to chose? How can I have a good option? Any
suggestion? Or any articles available?
I guess
Dear gmx users,
Imagine it's a protein-membrane system which GROMOS53a6 and CHARMM36 will give
me the same acceptable output for it. Now if I want to choose one, what am I
supposed to chose? How can I have a good option? Any suggestion? Or any
articles available?
I guess the CHARMM FF is
On Fri, May 18, 2012 at 12:38 PM, Javier Cerezo j...@um.es wrote:
Hi Steven
You've tried with constraints = none, but that still keeps constraints
over water molecules through SETTLE algorithm. Maybe you can try a
minimization with define = -DFLEXIBLE to remove settle over water and
then
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor and will soon be leaving for a trip and will have limited access
to email, so relying on me for personal help is a bad choice at this time.
On 5/18/12 9:30 AM, Sarath Kumar Baskaran wrote:
Dear
I have a fully fluorinated alkane, and am wondering how to choose the right
atom-to-bead mapping. 4 CH2 groups form a C1 bead in Martini. Will CF2-CF2
(6 heavy atoms), also map to a C1 bead type? How does one go about making
the right choice? Reading the paper suggests that one has to make
Hi Guys
Could you please explain to me how to use the g_dipole method to calculate the
dipole moment of a Solute in a solvent.
Thanks alot
Milinda Samaraweera
University of Connecticut
Department of Chemistry
55 N Eagleville road
unit 3060
Storrs CT
USA--
gmx-users mailing list
Dear Gromacs users,
I am using tabulated potentials for the dihedrals
of my system, the dihedral function I am using is Summn over 'n' 0.5*K [
( Cos n(phi-phi0)] , Here 1= n = 3 .
The C-O-C-C dihedral of my system has three folds those are n= 1 , 2, 3
and three
Hi everybody,
I'm working with a mixed membrane for the first time (POPC+POPE), and I want to
restrain the all phosphors (only Z axis).
However they belong to different [ moleculetype ] (ie. POPC and POPE), and
GROMACS does not restrain more than one molecule type at a time.
What implications
Dear GMX users,
I cannot figure out from the manual whether it is possible to use tabulated
non-bonded potentials in a BAR calculation.
I want to estimate the free energy for changing Fe2+ to Fe3+. These have
different charges, of course, and also different non-bonded interactions.
These
Why dont you create index files of whatever types you want and then just use in
your mdp:
freezgrps (from index) and the corresponding directions N N Y
Jan
On 18 May 2012, at 20:56, Ricardo O. S. Soares ross_...@yahoo.com.br wrote:
Hi everybody,
I'm working with a mixed membrane for the
Hi gmx-users,
I have a question might be explained before but I cannot understand from
the previous , how to calculation the intermolecular h-bonds between two
molecules? I saw someone mentioned using a second tpr file, but how to do
it specifically? Thanks very much!
Ja
--
gmx-users mailing
On 5/18/12 3:56 PM, Ricardo O. S. Soares wrote:
Hi everybody,
I'm working with a mixed membrane for the first time (POPC+POPE), and I want to
restrain the all phosphors (only Z axis).
However they belong to different [ moleculetype ] (ie. POPC and POPE), and
GROMACS does not restrain more
On 5/18/12 4:21 PM, Rustad, James R wrote:
Dear GMX users,
I cannot figure out from the manual whether it is possible to use tabulated
non-bonded potentials in a BAR calculation.
I want to estimate the free energy for changing Fe2+ to Fe3+. These have
different charges, of course, and also
On 5/18/12 7:22 PM, mu xiaojia wrote:
Hi gmx-users,
I have a question might be explained before but I cannot understand from the
previous , how to calculation the intermolecular h-bonds between two molecules?
I saw someone mentioned using a second tpr file, but how to do it specifically?
Thank you very much Patrick. This is exactly what I was looking for. Based on
what you sent, I'm going to go with the following text in my work:
The value of tau_int is approximately half of the amount of time required, on
average, to obtain a statistically independent (decorrelated) sample
Dear Shima:
I don't believe that anybody knows what lipid forcefield is best for the study
of ion conduction through a membrane channel, or if it even matters. My
instinct is that, for the timescales that you are likely going to use, the
particular lipid forcefield that you select is not going
Dear Erik:
I thought about your comment for a while and I have come to understand that you
are correct. The exponential (or integral) autocorrelation time is a
mathematical construct and is defined as such. What I was looking for was an
interpretation of the autocorrelation time in terms of
On 5/18/12 10:28 PM, Peter C. Lai wrote:
Synopsis: position restraints are coupled to the moleculetype. So you need to
define position restraints individually for each molecule type contiguous
with their topologies.
There's a couple of ways to do it, using some simple #include and #define:
Thanks for the corrections. I had to mock up parts of it because usually
I only POSRE_RECEPTOR and POSRE_LIGAND. I also have a mix of putting the
position restraints in .itp file vs. in the topol.top, depending on how often
I am changing my topol.top (things like genion and g_membed modify them).
Dear Christopher,
Thanks for your kind reply. :-)
Sincerely,
Shima
From: Christopher Neale chris.ne...@mail.utoronto.ca
To: gmx-users@gromacs.org gmx-users@gromacs.org
Sent: Saturday, May 19, 2012 6:19 AM
Subject: [gmx-users] forcefields for lipids
Dear
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