The problem I was facing earlier: in the force field files (I am ussing
ffG53a6) the ions are named NA+, CL-, for example, so with capital letters.
Genion will add to the topology the ions named by default Na or Cl, unless
you use the options -pname and/or -nname to name the ions. I do so and I
hav
Dear gmx-users,
I am try to simulate the protein-drug, and have used drg.itp from prodrg
server2,5(beta). I have also got pro.top from pdb2gmx programs. But when I
issue a grompp command for minimization,grompp gives a fatal error.
The error is:
Error 0 [file "unk.itp",line 4]
Not enough para
Mark Abraham ha scritto:
> ms wrote:
>> Hi,
>>
>> I would like to understand a basic question about the usage of tabulated
>> potential for non-bonded interaction. If I use an arbitrary function and
>> I write a table for it, is the functional shape then applied to *all* my
>> atoms, or can I speci
qing yang wrote:
Dear gmx-users,
I am try to simulate the protein-drug, and have used drg.itp from prodrg
server2,5(beta). I have also got pro.top from pdb2gmx programs. But when
PRODRG topologies are often unsatisfactory with respect to charges and charge
groups assigned. Looking at the
Is the decrease occurs in the long times? Omer.
On Tue, Nov 17, 2009 at 21:08, Chih-Ying Lin wrote:
>
>
>
> HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I
> simulate the protein and ligand system and then calculate the MSD of the
> ligand. Then, i drew the plot of the tim
Hi
I am trying to open a gromacs .gro file with VMD but
VMD gives the following message upon opening and does not display the
molecule : [ error reading box , unexpected end-of-file reached ]
I checked number of atoms specified on the second line of the gro file
and number of atoms really presen
leila karami wrote:
Hi
I am trying to open a gromacs .gro file with VMD but
VMD gives the following message upon opening and does not display the
molecule : [ error reading box , unexpected end-of-file reached ]
I checked number of atoms specified on the second line of the gro file
and
dear justin
I checked the VMD mailing list but that does not help me.
first few lines of my gro file :
Protein in water
23136
1GLY N1 1.655 4.898 3.866 -0.3222 -0.2420 0.1437
1GLY CA2 1.677 4.774 3.793 0.0134 -0.2201 0.2050
1GLYHA13 1.579 4
You include unk.itp but show us drg.itp. Perhaps you're looking at or
using the wrong file.
/Erik
qing yang skrev:
Dear gmx-users,
I am try to simulate the protein-drug, and have used drg.itp from
prodrg server2,5(beta). I have also got pro.top from pdb2gmx programs.
But when I issue a gro
leila karami wrote:
dear justin
I checked the VMD mailing list but that does not help me.
first few lines of my gro file :
Well, the structure of the .gro file appears intact. Somewhere along the way,
VMD thinks it's hitting the end of the file. Have you manipulated or edited the
fi
2009/11/18 qing yang
> Dear gmx-users,
>
> I am try to simulate the protein-drug, and have used drg.itp from prodrg
> server2,5(beta). I have also got pro.top from pdb2gmx programs. But when I
> issue a grompp command for minimization,grompp gives a fatal error.
>
> The error is:
>
> Error 0 [f
Hello,
Did you try to just add a blank line at the end of the file? (after the
box definition). Sometimes, that works for me. Otherwise, it could a
problem of bad end-of-line character. That may happen if you have edited
the file on Windows and try to visualize it on Linux.
Nicolas
leila ka
dear justin
I transfer gro files from linux to windows through SSH secure shell program.
I added 10 Na ions by genion command but in gro file following case is
appeared:
7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991
7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.182
leila karami skrev:
dear justin
I transfer gro files from linux to windows through SSH secure shell
program. I added 10 Na ions by genion command but in gro file
following case is appeared:
7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991
7209Na Na23128 0.179 2
Erik Marklund skrev:
leila karami skrev:
dear justin
I transfer gro files from linux to windows through SSH secure shell
program. I added 10 Na ions by genion command but in gro file
following case is appeared:
7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991
7209Na
leila karami wrote:
dear justin
I transfer gro files from linux to windows through SSH secure shell
program. I added 10 Na ions by genion command but in gro file following
case is appeared:
If an unrequested Cl is being added, then that is worth investigating. What was
your *exact* ge
They are published in the paper by smith et al. (J. Phys. Chem. B 2004,
108, 1065-1071) and have also been posted previously on this mailing list
(both of which can be found through a simple search). Please note that the
parameters posted on the mailing list are not quite correct as they have
t
Hi Berk,
I have done the tests and you are entirely correct. I have one further
question: If I simply want to pull to a relative displacement of -1.0
nm, is there any reason to prefer one of these methods, or are they
just overlapping implementations of different methods that also have
un
Hi,
With only 1 pull dimension active (through pull_dims) all three geometries are
equivalent.
In 2 or 3D there are all different.
With pull_geometry=direction the pull force is the force working along the
direction vector.
So in general you can't incorporate the direction (only sign in your c
Hi all,
i tried out the constant_force pulling, to simulate a force clamp
pulling experiment. But there are now some questions. But first describe
the system and so on...
The system consists of two molecules which can bind through hydrogen
bonds with no water. Each molecule has one atom which w
Hi,
I think you mis-read the manual.
With constant-force there is no reference position (since a linear potential
has no reference point),
but you can, and in your case should, use a reference group.
Then you can also use the geometry distance.
Berk
> Date: Wed, 18 Nov 2009 19:08:43 +0100
> Fr
Dear All:
I'm new to Gromacs. I want to simulate water disolve in fatty acid
(C-C-COOH) using a all atom model. I started up with constructing the pdb
file of decanoic acid. Following the post by Justin
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I added
the [Eth] and
Tengfei Luo wrote:
Dear All:
I'm new to Gromacs. I want to simulate water disolve in fatty acid
(C-C-COOH) using a all atom model. I started up with constructing the
pdb file of decanoic acid. Following the post by Justin
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I
Justin:
Thank you for your help!
Yes, the OH bond length changed before and after minimization. and yes, the
H get close to the carbonyl O in the COOH group. I did the minimization with
solvent.
I appreciate any further suggestion!
Tengfei
- Original Message -
From: "Justin A. Lem
Tengfei Luo wrote:
Justin:
Thank you for your help!
Yes, the OH bond length changed before and after minimization. and yes,
the H get close to the carbonyl O in the COOH group. I did the
minimization with solvent.
I appreciate any further suggestion!
Can you post your .mdp file? I have
Here it is:
title = acid
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXIBLE ; use flexible water model
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_n
When I run grompp using all your files, I get a series of errors:
ERROR 1 [file topol.top, line 60]:
No default Bond types
ERROR 2 [file topol.top, line 144]:
No default Angle types
ERROR 3 [file topol.top, line 190]:
No default Ryckaert-Bell. types
ERROR 4 [file topol.top, line 191]
Justin:
Thank you very much! It worked and everything seems reasonable now.
Regards,
Tengfei
- Original Message -
From: "Justin A. Lemkul"
To: "Gromacs Users' List"
Sent: Wednesday, November 18, 2009 2:47 PM
Subject: Re: [gmx-users] how to construct fatty acid
When I run grompp
Sarah Witzke wrote:
> Dear gmx-users,
>
>
>
> I have done simulations of one small molecule that diffuses into a DMPC
> membrane. This small molecule contains an alcohol group and is therefore
> capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol
> region).
>
> I have read th
Hi
The MSD decrease occurs in the long times.
The ligand has bounded to a protein.
How can the decrease happen?
Thank you
Lin
Chih-Ying Lin wrote:
>
>
>
> HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I
> simulate the protein and ligand system and then calculate the MSD
Sarah Witzke wrote:
Yes, I see this. Do you by the way know why this .ndx files under the title [ donors_hydrogens_DMPC ] lists a lot of non-heteroatoms (carbon atoms)?
No clue. Probably the code identifies the functional group to which the donor
belongs. The more pertinent directiv
Chih-Ying Lin wrote:
Hi
The MSD decrease occurs in the long times.
The ligand has bounded to a protein.
How can the decrease happen?
Probably because the ligand, being bound to the protein, has its motion
restricted by its interaction with the protein. I don't see the purpose of
measuring
Sarah Witzke wrote:
>
> Yes, I see this. Do you by the way know why this .ndx files under the title [
> donors_hydrogens_DMPC ] lists a lot of non-heteroatoms (carbon atoms)?
>
No clue. Probably the code identifies the functional group to which the donor
belongs. The more pertinent directi
Sarah Witzke wrote:
ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per
hbond is 628.571 ps?
Yes, per the calculation. For a bit more about the analysis, see the "Please
read and cite" notices, as well as this thread:
http://lists.gromacs.org/pipermail/gmx-users/2
Sarah Witzke wrote:
> ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per
> hbond is 628.571 ps?
>
Yes, per the calculation. For a bit more about the analysis, see the "Please
read and cite" notices, as well as this thread:
http://lists.gromacs.org/pipermail/gmx-use
Sarah Witzke wrote:
Sarah Witzke wrote:
ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per
hbond is 628.571 ps?
Yes, per the calculation. For a bit more about the analysis, see the "Please
read and cite" notices, as well as this thread:
http://lists.gromacs.o
Dear All,
I started a protein simulation for 100ps with octahedron box. After
completion of that run I visualized the protein at the centre of the
octahedron box by using trjconv.
Then I have extended the simulation for another 500 ps by using tpbconv.
But now it is showing as cubic box when I
On Wed, Nov 18, 2009 at 9:29 PM, sukesh chandra gain wrote:
> Dear All,
> I started a protein simulation for 100ps with octahedron box. After
> completion of that run I visualized the protein at the centre of the
> octahedron box by using trjconv.
> Then I have extended the simulation for another
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