Sam Moors wrote:
Hi gmx users/developers,
I would like to do a molecular dynamics simulation with a restraint on
the backbone RMS deviation from a reference structure.
Does anybody know if this is possible?
Not exactly as you describe, but you should read the section in chapter
4 of the man
Vishwanath Dalvi wrote:
Thank you for your response. I am still unclear as to how the whole
thing works (and the manual is no help).
If I do specify (in the .mdp file) something like constraints =
all-bonds, will that override the harmonic-bond interactions specified
in the .itp files?
Do
Ángel Piñeiro wrote:
Dear all,
I have some membrane protein systems running in our cluster using
gmx4.0.4. The minimizations finish with reasonable potential energy
values (of the order of 10^-5 with maximum forces of the order of
10^-3). Then I am trying to run several 1-ns-long equilibration MD
There is a periodic dihedral within ffoplsaabon.itp which points to a reference.
Perhaps these are the parameters you are referring to. If not, check out the
bottom of ffoplsaabon.itp and read that paper to see if the parameters will suit
your needs.
If you need an R-B dihedral, you may ha
Chih-Ying Lin wrote:
Hi
how to make the different and specific displacement of ligand around
protein with GROMACS?
Use editconf: place the protein and ligand in a box of the same dimensions.
Specify the center for each molecule, and concatenate the ligand and protein
.gro files.
-Jus
Hi
how to make the different and specific displacement of ligand around protein
with GROMACS?
i only know how to make the ligand randomly displaced around protein.
Thank you
Lin
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They are CH3-SI-O-SI, SI-O-SI-CH3 and SI-O-SI-O. I have looked up
ffoplsaabon.itp. it doesn't include any dihedral consisting of SI. And the
literatures only have the parameters for periodic potential. Thank you so
much for your kind help!
On Fri, May 15, 2009 at 4:00 PM, Justin A. Lemkul wrote:
Yanmei Song wrote:
Yes, I have read that part and still have no idea how can I do that.
That part tells us how to transfer from the OPLS parameters Vi to RB
potential in GROMOS force field Ci. Now what I have is phi and k for
periodic potential. Is there any way I can get Ci for RB potentia
Yes, I have read that part and still have no idea how can I do that. That
part tells us how to transfer from the OPLS parameters Vi to RB potential in
GROMOS force field Ci. Now what I have is phi and k for periodic potential.
Is there any way I can get Ci for RB potential from phi and k in order
Please keep all Gromacs-related correspondence on the gmx-users list. That way,
the discussion is archived for the later benefit of others, and you have a
chance to reach a wider audience of individuals who may be able to help you.
That said, read the manual, section 4.2.12.
-Justin
Yanmei
bohumir wrote:
Dear GROMACS Masters,
is there a trick to obtain coordinates and velocities of center of
mass of each water molecule?
Have a look at g_traj, although to analyze each molecule separately could take
many iterations with specific index groups.
-Justin
Currently, the positio
Dear Justin:
If I have the parameters of GROMOS force field for the proper dihedral,
which i think they are phi and k for function 1 for periodic type. I wanted
to use OPLS force field. As far as I know in OPLS the dihedral was RB
potential in fuction 3. So my question is do you know any method I
Quoting bohumir :
Dear GROMACS Masters,
is there a trick to obtain coordinates and velocities of center of
mass of each water molecule?
Currently, the positions and velocities of *each individual atom* of
all water molecules are written to the "traj.trr" file.
I would like to look at velocity p
Dear GROMACS Masters,
is there a trick to obtain coordinates and velocities of center of
mass of each water molecule?
Currently, the positions and velocities of *each individual atom* of
all water molecules are written to the "traj.trr" file.
I would like to look at velocity profiles, but not tho
Thank you for your response. I am still unclear as to how the whole thing
works (and the manual is no help).
If I do specify (in the .mdp file) something like constraints = all-bonds, will
that override the harmonic-bond interactions specified in the .itp files?
_
Yanmei Song wrote:
Dear Justin:
Thank you for your suggestions. using shift for vdwtype helps a lot.
Can I ask you another question? The density of my system is about 8%
larger than the experimental value. Do you have any suggestions on how
to reduce the density of the system. Or once the f
Dear Justin:
Thank you for your suggestions. using shift for vdwtype helps a lot.
Can I ask you another question? The density of my system is about 8% larger
than the experimental value. Do you have any suggestions on how to reduce
the density of the system. Or once the force field and all the pa
วันเวลา อมรนพ wrote:
Dear gmx users
I want to simulate propane molecule and I use PRODGE website to generate
both .gro and .top file.
Then I run the grompp program and there is an error said that
Fatal error:
Invalid order for directive moleculetype, file ""topol.top"", line 17
and below
Dear gmx users
I want to simulate propane molecule and I use PRODGE website to generate
both .gro and .top file.
Then I run the grompp program and there is an error said that
Fatal error:
Invalid order for directive moleculetype, file ""topol.top"", line 17
and below is my topology file of a prop
Dear sir :
Can you give me some information on Combined essential dynamics analysis and
its procedure?
Thank you!
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Jussi Lehtola wrote:
Hi,
I wonder who has written the xdrfile software, since there has been no
reaction to the bug I opened at
http://bugzilla.gromacs.org/show_bug.cgi?id=312
a month ago. Currently xdrfile does not fulfill its purpose as a
proprietary software -friendly package, since it co
Hi,
I wonder who has written the xdrfile software, since there has been no
reaction to the bug I opened at
http://bugzilla.gromacs.org/show_bug.cgi?id=312
a month ago. Currently xdrfile does not fulfill its purpose as a
proprietary software -friendly package, since it contains two headers
that
Hello Rolf,
There might be some issues with the exact format, below I pasted a record from
a standard pdb-file (that works with pdb2gmx) for comparison.
Otherwise for a simple molecule like methane, x2top is probably better suited
than pdb2gmx to generate the topology.
Best wishes
Andreas
> -
H
I think this a problem of bad format of your pdb file.
What is happening is that your CH4 is not in the right position, in the
pdb file, so pdb2gmx are just reading the letter C from your CH4.
Check carefully the pdb file format. You can try to remove two empty
spaces between ATOM and the residu
Hi gmx users/developers,
I would like to do a molecular dynamics simulation with a restraint on the
backbone RMS deviation from a reference structure.
Does anybody know if this is possible?
If yes, could you explain how to do it?
If no, what would be the easiest way to implement this in gromacs
Hello everybody,
I'm trying to set up a box with methane. Therefore I wrote a small pdb file
which looks like this:
ATOM 1 CH4CH4 11.0 1.0 1.0 1.0 0.0
ATOM 2 CH4CH4 20.5 0.5 0.5 1.0 0.0
ATOM 3 CH4CH4 3
Dear all,
I have some membrane protein systems running in our cluster using
gmx4.0.4. The minimizations finish with reasonable potential energy
values (of the order of 10^-5 with maximum forces of the order of
10^-3). Then I am trying to run several 1-ns-long equilibration MD
trajectories with prog
Hi,
The issue is slightly different here.
Currently TPI in Gromacs is limited to inserting a single charge group.
Since energy groups should consist of whole charge groups, the inserted
molecule can only consist of a single energy group.
You can solve your problem by making the whole inserted mol
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