Your starting topology is already broken if you have a non-integral total
charge that's larger than the magnitude for floating point errors (in your
case, .02 is floating point error, the 0.55 is systematic). Try figuring
out where the charge assignments went wrong (the qtot column in the
Dear Gromacs Users!
I'd like to change default protonation state of some specified Glu and Asp
residues im my protein.
By defaylt pdb2gmx -ignh create unprotonated state of the negatively
charged residues but I want to make 2 of such residues protonated to mimick
some intermollecular
Dear Gromacs users,
I minimized a protein structure 1IARcompleted_WT.pdb, getting, among
others, the files 1IARcompleted_WT_minimized.trr and
1IARcompleted_WT_minimized_potential_energy.xvg . Looking at the latter
file showed the last frame to be at 217 ps:
.
.
@ s0 legend Potential
Dunno but try with -timestep 1?
Anyway, the .gro file emitted by mdrun contains the last frame anyway,
so there's not much reason to use trjconv to dump the last frame in the
first place...
On 2012-02-13 04:19:45PM +0200, Ehud Schreiber wrote:
Dear Gromacs users,
I minimized a protein
Hi,
sorry I'm back to this thread after quite a long time, as I was trying
to solve other problems. Now I'm back to the reverse transformation
tutorial on the martini webpage and whenever I try to use the mdp
script provided there for the annealing I just end up with the same
error message, which
On 2012-02-21 23:26, Broadbent, Richard wrote:
On 21/02/2012 19:02, David van der Spoelsp...@xray.bmc.uu.se wrote:
On 2/21/12 6:17 PM, Richard Broadbent wrote:
Dear All,
I am considering conducting a simulation of a polymeric system in
gromacs. I would like to use the COMPASS forcefield
Dear All,
We are pleased to announce the release of the program RESP ESP
charge Derive version III.5 (or R.E.D. III.5) and its related tools
(Ante_R.E.D.-1.5 and X R.E.D. III.5) available @
http://q4md-forcefieldtools.org/RED/.
New features available:
- Bug corrections and code
Dear Dr. Warren,
Thank you very much from your response.
When I see the coordinate file, there is a box consists of water in half of it
and another half of box is void, but when I do md.mdp for production
simulation, all of water molecules are dispersed in total of box.
Can you help me for
Dear Mark,
Thank you very much from your reply.
I see a box that the half of it consists of water and another half of box is
void, but when I run md.mdp for production simulation all of water molecules
dispersed in total of box and I don't see interface and total of box filled by
water.
Can
Dear Justin,
thakn you for your answer, although it is quite discouraging...
g_mindist is only partially suitable for my scope: it gives me the number of
contacts, and also the residues that contact the ligand at least once in the
simulation (if I use -or in addition to -od), but with g_hbond I
James Starlight wrote:
Dear Gromacs Users!
I'd like to change default protonation state of some specified Glu and
Asp residues im my protein.
By defaylt pdb2gmx -ignh create unprotonated state of the negatively
charged residues but I want to make 2 of such residues protonated to
mimick
Thanks Justin.
Your aproach is very usefull indeed.
I've just one relative question about CAPPING of the termi in the case of
simulation of the membrane receptors. In that proteins both of N and C
termi are in the water polar layer. In the literature I've found nothing
about capping of the
Dear Gromacs Users!
I want to perform simulation of the membrane receptor in the membtane
environment. There are some evidence about precense of the
functional-relevant internal water mollecules in the transmembrane
alpha-helix bundle of the receptor.
I want to take into account that internal
James Starlight wrote:
Thanks Justin.
Your aproach is very usefull indeed.
I've just one relative question about CAPPING of the termi in the case
of simulation of the membrane receptors. In that proteins both of N and
C termi are in the water polar layer. In the literature I've found
Dear gromacs users,I have a comprehension question to g_dist with the lifetime(-lt) option.I want to determine the lifetime of a certain sidechain - ion contact (I use all ions as a group) within a radis of 0.6 nm.output:@ title a_538 - K within 0.6 nm@ xaxis label Time (ps)@ yaxis label Number of
Dear Gmx Users, Dear Justin,
I run pulling of my ligand away from my protein. Then I used Justin perl
script to extract distances for umbrella sampling windows between my ligand
and crucial residue of my protein (Isoleucine). The number of hydrogen
bonds between ligand and protein during the
Steven Neumann wrote:
Dear Gmx Users, Dear Justin,
I run pulling of my ligand away from my protein. Then I used Justin perl
script to extract distances for umbrella sampling windows between my
ligand and crucial residue of my protein (Isoleucine). The number of
hydrogen bonds between
Thank you!
On Wed, Feb 22, 2012 at 4:08 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Gmx Users, Dear Justin,
I run pulling of my ligand away from my protein. Then I used Justin perl
script to extract distances for umbrella sampling windows between my ligand
and
Dear Gromacs Users,
I am interested in opportunities to simulate protein transition from active
to passive state.
Exists a possibility to put into Gromacs two states of protein and forced the
transition from
state A to B? Measuring by the way the energy of the frame state? I will be
Dear gromacs users,
I am adding a new residue to the existing
force field in gromacs for that i am using some new atom types i added
these atom types to the atomtypes.atp file and ffnonbonded.itp and I am
using Buckingham potential for the non-bonded interactions
Dear GROMACS users,
While simulating a DLPC membrane, I noticed that it tends to diffuse along
the normal (Z-axis) component. Is there a 'standard' restrain that is used
to prevent such diffusion?
The first option I thought was to restrain the center of mass of the whole
membrane along the
On 22/02/2012 11:17 AM, NG HUI WEN wrote:
*From:*NG HUI WEN
*Sent:* Sunday, February 19, 2012 1:19 PM
*To:* gmx-users@gromacs.org
*Subject:* Distance Restraints on Protein - possible at all?
Dear gmxusers,
I have been trying to apply distance restraints on my protein but have
been
On 22/02/2012 10:34 PM, mohammad agha wrote:
Dear Mark,
Thank you very much from your reply.
I see a box that the half of it consists of water and another half of
box is void, but when I run md.mdp for production simulation all of
water molecules dispersed in total of box and I don't see
On 23/02/2012 6:02 AM, ramesh cheerla wrote:
Dear gromacs users,
I am adding a new residue to the
existing force field in gromacs for that i am using some new atom
types i added these atom types to the atomtypes.atp file and
ffnonbonded.itp and I am using
On 23/02/2012 10:26 AM, Jose Borreguero wrote:
Dear GROMACS users,
While simulating a DLPC membrane, I noticed that it tends to diffuse
along the normal (Z-axis) component. Is there a 'standard' restrain
that is used to prevent such diffusion?
The first option I thought was to restrain the
Dear Mark,
Thanks for contributing your ideas and suggestions, really appreciate it.
The reason I am playing with distance restraints on my protein is because I am
interested to see the effects of equilibrating a protein in membrane using the
two different restraint methods i.e. distance vs.
Dear Mark,
Thank you very much from your reply.
Best Regards
Sara
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thursday, February 23, 2012 5:24 AM
Subject: Re: [gmx-users] interface
On
Hi GROMACS users,
I wish to study proteins behaviour,With the help of command
genbox -ci protein.gro -nmol no of protein .. -box box size
-o out put file -p topology file I am putting the four peptide
at random positions, but I need to put theem close enough so they
are forming at least one
On 23/02/2012 5:46 PM, rama david wrote:
Hi GROMACS users,
I wish to study proteins behaviour,With the help of command
genbox -ci protein.gro -nmol no of protein .. -box box size
-o out put file -p topology file I am putting the four peptide
at random positions, but I need to put theem close
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