Dear users,
I just wanted a small clarification whether the order of elements in matrix
(-hbm) corresponds to reverse order of elements in the index file (-hbn)
obtained from g_hbond?
Thank you
Kavya
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gmx-users mailing listgmx-users@gromacs.org
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Thanks a lot of suggestions. Now my simulation is running without any
errors.
I have decreased the box dimension (by using -d 1.2 in editconf) and also
by using cutoff with
rlist=rvdw=rcoulomb=1.0. Now there is no warning or errors in nvt and npt
equilibration.
Thank you,
with regards,
Anu
On Th
On 2/21/13 8:19 PM, Juliette N. wrote:
Hi Justin,
When one issues g_energy –f *.edr –nmol X –b XXX, g_energy reads the frames
from -f edr. file which is already written each nstenergy = 1000 steps for
instance. So g_energy is not reading all MD steps. and I guess the same
steps are printed to
Hi Justin,
When one issues g_energy –f *.edr –nmol X –b XXX, g_energy reads the frames
from -f edr. file which is already written each nstenergy = 1000 steps for
instance. So g_energy is not reading all MD steps. and I guess the same
steps are printed to .xvg as out of g_energy. Please help me rea
Thank Erik and Dallas so much !
I got it :-)
On Fri, Feb 22, 2013 at 4:53 AM, Dallas Warren wrote:
> If you have a particle at 1.000 1.000 1.000
>
> If use editconf -translate 0 1 -1
>
> Then that particle will be moved to 1.000 2.000 0.000
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Discovery Bi
On 2/21/13 7:35 PM, Mehdi Bagherpour wrote:
Thanks Justin
I have any question?
i will use minimization with this restrain.
using genrestr I make min.itp.
how should I use this .itp file in grompp or mdrun?
As you would any other .itp file; #include it in the topology, within the
corres
Thanks Justin
I have any question?
i will use minimization with this restrain.
using genrestr I make min.itp.
how should I use this .itp file in grompp or mdrun?
On Fri, Feb 22, 2013 at 2:41 AM, Justin Lemkul wrote:
>
>
> On 2/21/13 6:09 PM, Mehdi Bagherpour wrote:
>
>> I am using Gromacs
On 2/21/13 6:58 PM, Juliette N. wrote:
Hi Matthew,
Thanks for your reply. I tried g_analyze as you suggested:
1) I am wondering why the average given by g_energy and g_analyze are not
identical. I tried the following:
g_energy -f Potential. edr -o Potential.xvg and extracted the average the
On 2/21/13 6:30 PM, Elisabeth wrote:
Thanks Justin. Can you please elaborate on why for a binary
(solute+solvent) the size should be larger than 2 Rc? I thought minimum
image convention works for all atoms (solute ans solvent) and this makes
sure forces are not double-counted. What if the solut
On 2/21/13 6:24 PM, Yun Shi wrote:
So in umbrella sampling, does it really matter if the vector
connecting the COMs of protein and ligand is NOT parallel with the
vector of the pulling force (although the pull rate is 0)?
I guess as long as the force in each sampling window is along the same
d
Hi Matthew,
Thanks for your reply. I tried g_analyze as you suggested:
1) I am wondering why the average given by g_energy and g_analyze are not
identical. I tried the following:
g_energy -f Potential. edr -o Potential.xvg and extracted the average then
provided Potential.xvg as input to g_anal
Thanks Justin. Can you please elaborate on why for a binary
(solute+solvent) the size should be larger than 2 Rc? I thought minimum
image convention works for all atoms (solute ans solvent) and this makes
sure forces are not double-counted. What if the solute is a polymer, I mean
how can one calcul
So in umbrella sampling, does it really matter if the vector
connecting the COMs of protein and ligand is NOT parallel with the
vector of the pulling force (although the pull rate is 0)?
I guess as long as the force in each sampling window is along the same
direction, we can in theory get potentia
On 2/21/13 6:10 PM, Elisabeth wrote:
Hello everyone,
Does anyone know if the minimum image convention has something to do with
the box size effect (independence of simulation results from system size) ?
i.e. When the box size is larger than 2*r_c, does this ensure that the
results are independ
On 2/21/13 6:09 PM, Mehdi Bagherpour wrote:
I am using Gromacs software for DNA simulation. Specially in my project I
need to fix two ends base pairs of DNA,The DNA that I want to simulate has
12 sequence shown bellow
5-- *C*GCAACG*C* --3
3-- *G*CGTTGC*G* --5
I dont know how I can us
If you have a particle at 1.000 1.000 1.000
If use editconf -translate 0 1 -1
Then that particle will be moved to 1.000 2.000 0.000
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war..
Perfect! Everything worked, thanks to all that helped -- I really
appreciate it.
Amit
On Thu, Feb 21, 2013 at 2:00 PM, Erik Marklund [via GROMACS] <
ml-node+s5086n5005774...@n6.nabble.com> wrote:
> Hi,
>
> For an analysis tool you would use the functions in tpxio.h for
> reading tpr files. The
Hi,
For an analysis tool you would use the functions in tpxio.h for
reading tpr files. Then you don't need to bother about filling out the
inputrec yourself.
Erik
On Feb 21, 2013, at 7:48 PM, shavit wrote:
I think your'e right. I'm currently trying to make it work, but am
not
really s
Check gmx_energy.c. It contains this line:
read_tpx(topnm, &ir, box, &natoms, NULL,NULL, NULL, &mtop);
where ir is t_inputrec.
Reid
On Thu, Feb 21, 2013 at 1:48 PM, shavit wrote:
> I think your'e right. I'm currently trying to make it work, but am not
> really succeeding. I'm declaring t_in
I think your'e right. I'm currently trying to make it work, but am not
really succeeding. I'm declaring t_inputrec *ir, and then trying to
reference ir->delta_t. Even in compile-time, I get a warning that delta_t
is being used without being initialized, which makes sense. Is there any
function
On 2/21/13 10:18 AM, shahid nayeem wrote:
Dear all
I want to simulate a protein complex with 4 chains two of which is
linked with disulfide bonds. Does this simulation requires that all
chains are merged into one molecule definition or I should merge only
two chains which are linked with disulf
On 2/21/13 9:47 AM, shavit wrote:
Hello,
For several months now, I've been writing my own analysis tools using the
GROMACS template.c file. There is one thing I haven't been able to figure
out, and that is how to get the timestep size.
I'm confident this parameter is located in either the tr
On 2/21/13 12:33 AM, bipin singh wrote:
Hello All,
I want to know how to mention a group (group2) without any temperature
coupling in mdp file. From the manual I got to know that we should mention
tau_t= -1 for no temperature coupling. And in the ref_temp section I have
mention two values, 300
On 2/21/13 12:00 AM, aixintiankong wrote:
Dear,
there are three waters in active site of receptor,mediating the binding of
ligand with target protein. i want to study the three waters how to affect the
binding of ligand with target protein and the contribution to the stability of
the sy
Hi Vedat
You are right. I think that a oligonucleotide with both 5' and 3' phophates
can be simulated,
but probably the charge density is too high (for instance a dodecamer would
carry a negative charge
of 26 instead of 22 in the regular definition or 24 if the 5' phosphates
are explicitly taken
i
hi paulo & gmx,
thank you for your time and hint! as far as i've understood from your
paper which was interesting to read, you mainly modelled 5'-phosphate
molecules?
anyways, since we intended to simulate a 3'-terminal phosphate as well,
we just created a phosphate residue by modifying the
Hi,
I don't know of a GROMACS tool to do this. g_analyze may work (see manual
page, option "-ee"), if you can generate a time series of A to look at.
That said, what you've described is a classic propagation of error problem.
If uncertainties are small and likely to be symmetric about the mean, t
Hi,
What difference does it make? All coordinates are translated by a
fixed vector. There is no need for a reference point.
Best,
Erik
On Feb 21, 2013, at 3:31 PM, Kieu Thu Nguyen wrote:
Dear all,
I am not clear about the option -translate following editconf tool.
Whether the coordinates
I know this is quite an old topic, but thank you for all of your help!
I ended up just hard-coding the bonds into the code, which is not ideal, but
it is what it is.
Thanks again,
Amit
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Extracting-bond-information-from-topol-tp
Hello,
For several months now, I've been writing my own analysis tools using the
GROMACS template.c file. There is one thing I haven't been able to figure
out, and that is how to get the timestep size.
I'm confident this parameter is located in either the traj.trr file or the
topol.tpr that I fe
On Feb 20, 2013, at 9:58 PM, Erik Marklund wrote:
Hi,
pdb2gmx generate the connectivity from the residue and atom
sequences (the file format specs state the order in which they
appear) and the distances between atoms. This is fairly robust as
long as the coordinates aren't unusually bad.
Hi Ahmet,
What is an incorrect RMSD? What is a correct RMSD? If you want to
calculate a backbone RMSD and you include side chain atoms, that's
wrong. Likewise, if you want to calculate a heavy atom, or
protein-all-atom RMSD and include virtual sites, that's wrong. If you
want to calculate an all-p
Dear Tsjerk,
Do the virtual sites cause incorrect calculations of SASA, RMSD or something
else?
Regards
2013/2/21 Tsjerk Wassenaar
> Hi Ahmet,
>
> You can always use suitable index groups for analysis.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım
> wrote:
> > I th
Hi Ahmet,
You can always use suitable index groups for analysis.
Cheers,
Tsjerk
On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım wrote:
> I thought the virtual sites can affect analysis.For example, dont they cause
> incorrect calculations of SASA, RMSD or something else?
>
> Thanks in advance
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