Dear Gmx Users,
I want to obtain average Protein-Ligand SR electrostatics and LJ energy
values using g_energy from NPT equlibration with position restraints. I
used
energygrps = Protein LIG
However, when I run g_energy -f npt.edr -s npt.tpr
I see neither Protein-LIG for any of them. Would you
and the molecule to which it is tethered
need to be in the same [moleculetype], so run pdb2gmx (or whatever you are
using) with care.
-Justin
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Thank you for this. And also I wish to attach a chain
...@vt.edu wrote:
On 10/10/13 9:21 AM, Steven Neumann wrote:
How about applying position restarints with a strong force constant? What
is less computationally expensive: position restrained, freezing the whole
molecule? The nanotube should be rigid... Shall I place the edged of the
You
And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is
there any gmx tool to exclude interactions within the given molecule so 1
with all 1200, 2 with all 1200...etc... 1200 with all 1200?
Steven
On Thu, Oct 10, 2013 at 2:34 PM, Steven Neumann s.neuman...@gmail.comwrote
, 2013 at 2:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 9:34 AM, Steven Neumann wrote:
Thanks a lot. You the bond as a distance between atoms? I wish to avoid
bonds as they are not necessary...just position restraint. What would be
the force constant? I tried 1000 once without bonds
Thank you. Would both be equal in terms of gaining computational time?
Steven
On Thu, Oct 10, 2013 at 2:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 9:39 AM, Steven Neumann wrote:
And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] -
is
there any gmx tool
Thank you. I do not have any explicit solvent in my system. I included the
solvent in nonbonded parameters so not even implicit.
Steven
On Thu, Oct 10, 2013 at 2:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 9:44 AM, Steven Neumann wrote:
Thanks. I will place them then within
Thanks a lot. I will use position restraints then with a strong force
constant, no bonds and place the edge atoms within half of distance between
them from the box edge. Is that correct?
Steven
On Thu, Oct 10, 2013 at 2:56 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 9:54 AM, Steven
Thank you!
Steven
On Thu, Oct 10, 2013 at 3:02 PM, Justin Lemkul jalem...@vt.edu wrote:
On 10/10/13 10:01 AM, Steven Neumann wrote:
Thanks a lot. I will use position restraints then with a strong force
constant, no bonds and place the edge atoms within half of distance
between
them
Dear Gromacs Users,
I am trying to look for some references regarding the SMD. I found one
which tells about logarithmically dependency between the Rupture force
(maximum pulling force) obtained from SMD and the pulling rate. Just
wondering whether you are aware (or tested) the dependency between
Dear Gmx Users,
I have my carbon nanotube and I wish to make it infinite in lenght. Which
mdp options whall be used? pbc = xy and z is the infinite dimension?
another issue: Would you apply bonds between carbon atoms within the
nanotube or constraints using LINCS? Which of them is less
be (already) seen as neighboring. This looks the same as
the solvent molecule, one atom of which crossed the box boundary.
No?
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/26/13 8:39 AM, Steven Neumann wrote:
Dear Gmx Users,
I
DEa Users,
My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want
to use PME in my mdp:
rcoulomb = 2.0
coulombtype = PME
pme_order= 4
fourierspacing = 0.12
The cutoff needs to stay like this, I have my own tables with VDW, bonds,
angles
Thank you! Would you suggest just a cut-off for coulmb?
Steven
On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/4/13 10:03 AM, Steven Neumann wrote:
DEa Users,
My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I
want
to use PME in my mdp
Thank you. i am using my own vdw tables so need a cut off.
On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/4/13 10:11 AM, Steven Neumann wrote:
Thank you! Would you suggest just a cut-off for coulmb?
Not a finite one. The best in vacuo settings are:
pbc
Sorry it is a vacuum but I included implicit solvent in vdw parameters...So
I need pbc as well.
On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you. i am using my own vdw tables so need a cut off.
On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul jalem
Thanks a lot!
On Wed, Sep 4, 2013 at 3:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/4/13 10:44 AM, Steven Neumann wrote:
Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be
taken into account at infinite cutoff or omitted?
As I said, setting the cutoffs
Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be
taken into account at infinite cutoff or omitted?
On Wed, Sep 4, 2013 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/4/13 10:35 AM, Steven Neumann wrote:
I am not using any solvent. I mimic the presence
:20 AM, Steven Neumann wrote:
Sorry it is a vacuum but I included implicit solvent in vdw
parameters...So
I need pbc as well.
Sorry, this doesn't make much sense to me. If you're using implicit
solvent (GB), then it's by definition not vacuum. I also find the same to
be true - finite
Dear Gmx Users,
i wish I could restrain some ions in my system (NA). I tried to include it
in ions.itp:
[ moleculetype ]
; molnamenrexcl
NA1
#ifdef POSRES_NA
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
#endif
But it does not work.
Dear Gmx Users,
I run SMD to extract the windows for US calculations. The system involves
negatively charged ligand and protein. I generated the protein-ligand
complex within self assembly MD simulations.
I pulled my molecule away and two ions were also detached from the protein
surface being
binding?
It would be the ligand and two ions unless the ions also at some point
discossiate from the ligand once in solvent. Could add positional restraint
for them, but dont know how that effects the calculation?
*Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr
*Von:* Steven Neumann s.neuman
But even though on the other hand that could be more realistic free energy
which could be compare to experiment which also involves ions. Would Justin
please comment on this?
On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann s.neuman...@gmail.comwrote:
They do not dissociate...Are you sure? My
Thank you a lot!
On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/31/13 6:52 AM, Steven Neumann wrote:
But even though on the other hand that could be more realistic free energy
which could be compare to experiment which also involves ions. Would
Justin
please
I am do not want to choose different pulling conditions as I build a model
for specific force constant and pulling rate in given force filed. I think
restraining would help much more to then exclude the ions impact.
Steven
On Wed, Jul 31, 2013 at 12:49 PM, Steven Neumann s.neuman
Dear Gmx Users,
I want to run my simulations with tabulated non bonded and bonded
parameters on Gromacs 4.6.3. When I ask for 16 cpus it says:
that I am not able to use 16 or 8 with cut off scheme Group. So I set up
cutoff-scheme = Verlet
verlet-buffer-drift = 0.005
ERROR 1 [file grompp.mdp]:
Dear Users,
Can you please write me where gromacs does read the mass of each atom: Is
that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to
assign different mass for two different beads of the same type in my
topology.
Steven
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:
On 7/11/13 7:54 AM, Steven Neumann wrote:
Dear Users,
Can you please write me where gromacs does read the mass of each atom: Is
that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to
assign different mass for two different beads of the same type in my
topology.
It is taken
I have the same feeling, thank you. But in general mass can influence the
equilibrium property so I guess yes.
Steven
On Thu, Jul 11, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/11/13 8:17 AM, Steven Neumann wrote:
Thank you. Another question: Does RDF depends on the mass
Dear All,
Do you know how can I calculate angular distribution of all angles in my
system? Shall I specify in one index group all e.g. 80 atoms so g_angle
will calculate all possibile distributions and plot it as a sum?
Steven
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it as a function which will describe the
angular potential? Can I just refine and smooth it? But how I am going to
calculate the derivative?
Steven
On Mon, Jul 1, 2013 at 8:19 AM, Steven Neumann s.neuman...@gmail.comwrote:
Dear All,
Do you know how can I calculate angular distribution of all
Dear Gmx Users,
It is described how to use tabulated bonds/angles/dihedrals in 4.2.13
manual. I wish to use tables with angles table_a1.xvg, table_a2.xvg
However it is not described which function to use in [ angles ]. It is said
about [ bonds ] function 8 or 9 but no angles... Can anyone
Dear Users,
I know this error has been discussed many times but the outcome from
mdrun -pf and -px stopped at the same time which is 39470 ps. Somehow
gromacs caanot read pullx500.xvg but no clue why. I tried dos2gmx and still
the same error occur.
As I do not care about pullx500.xvg I run
space numbers, or
tab spacing, or etc...the only thing I noted was with xmgrace theirs a or
something at the end, but putting even this in manually to the files did
not work...dont know if that helps...
Stephan
*Gesendet:* Dienstag, 25. Juni 2013 um 10:48 Uhr
*Von:* Steven Neumann s.neuman
On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann s.neuman...@gmail.com
wrote:
On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 5:16 AM, Steven Neumann wrote:
Thank you
I will speak to someone who is familiar with the code. However, my Gromacs
version is installed on the cluster, can I create a file in my directory
which will use this code with a given potential?
On Wed, Jun 19, 2013 at 8:41 AM, Steven Neumann s.neuman...@gmail.comwrote:
On Tue, Jun 18
a GROMACS installation. Yet another reason to avoid modifying the C
code :-)
Mark
On Wed, Jun 19, 2013 at 10:06 AM, Steven Neumann s.neuman...@gmail.com
wrote:
I will speak to someone who is familiar with the code. However, my
Gromacs
version is installed on the cluster, can I create a file
On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 5:16 AM, Steven Neumann wrote:
Thank you.
Do you know whether it is possible to use the 5th order polynomial for
angles in Gromacs? I know I can use tables but wish to fit my data into
such a function
The constant angle has a weird units of kJ /mol rad^n while the angle is in
degrees. Does not make sense but at least I know where I made a mistake...
On Wed, Jun 12, 2013 at 10:43 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/12/13 10:01 AM, Steven Neumann wrote:
Dear Gmx Users,
I run
Whether it would be that easy i will find it. I specified my own potential
(not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed
h(x) in my table 6th column.
On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul jalem...@vt.edu wrote:
On 6/11/13 4:12 PM, Steven Neumann wrote
Dear Gmx Users,
Please, correct me if I am wrong. In ffnonbonded.itp
[ atomtypes ] - these are nonbonded parameters between atoms of the same
type
[ nonbond_params ] these are nonbonded parameters between atoms of
different type
[ pairtypes ] - 1-4 interactions
If that is correct why amber
Thank you. That means that e.g. when two LJ atoms of a different type
approaching each other the non bonded LJ potential energy is a sum of two
potentials of those atoms?
On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote:
On 6/12/13 5:30 AM, Steven Neumann wrote:
Dear
On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote:
On 6/12/13 6:00 AM, Steven Neumann wrote:
Thank you. That means that e.g. when two LJ atoms of a different type
approaching each other the non bonded LJ potential energy is a sum of two
potentials of those atoms
of freedom in T-Coupling group rest is 118.00
This run will generate roughly 2 Mb of data
So if I exclude 1-3 interactions I have the same number of nonbonded
parameters as well as 1-4 interactions. Can someone explain me this please?
On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman
An why do I have 1830 non bonded? 60*60/2 = 1800. There are 57 of 1-4
combinations so it should be lower than 1800...
And why 1830 1-4 interactions as I have only 57... Please, help/
Steven
On Wed, Jun 12, 2013 at 11:40 AM, Steven Neumann s.neuman...@gmail.comwrote:
I got it. However,
I
is not doing
a neighbor search!
Mark
On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com
wrote:
On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
grompp is just enumerating the possible combinations of parameters
given
your inputs
and 1830 1-4 interactions... there are 57 all possible 1-4 interactions
On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.comwrote:
All possible interactions = 60*60/2 = 1800. Where grompp takes another 30
from?
On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham
mark.j.abra
60 types of atoms and 60 atoms in total belonging to one residue
On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
How many atom *types* are there?
On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann s.neuman...@gmail.com
wrote:
and 1830 1-4 interactions
So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions
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Dear Gmx Users,
I run a simulation with quartic angle potential. These function has two
minima at 100 at 120 degrees. However, seems from my simulation that it is
not applied... all angles are around 180 degrees and my chain is a line
chain (straight).
I have in my topology
[ angles ]
; i j k
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:42 AM, Justin Lemkul wrote:
On 6/10/13 8:40 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:23 AM, Steven Neumann wrote:
Dear Gmx Users
Dear Gmx Users,
I am running CG simulation and I wish my beads to be constraint - one away
from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
have any bonds in my topology or rtp entry. I just add:
[ constraints ]
1 2 1 0.4
2 3 1 0.4
...
31 32
...@gmail.comwrote:
I think all is correct.
Why are you asking? People normally report problems.
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx Users,
I am running CG simulation and I wish my beads to be constraint - one
away
from each
Thank you Justin. So using nrexcl 0 or 1 (should be the same with
constraints) and type 1 will allow bonded atoms to interact (vdW) with each
other?
On Tue, Jun 11, 2013 at 6:10 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/11/13 10:46 AM, Steven Neumann wrote:
I was not sure about
Dear Gromacs Users,
I got really confused: In manual [defualts ]:
nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
(Buckingham)
I want to use mdrun -table table.xvg with my own potential, which one I
should choose?
gen-pairs - is for pair generation. The default is ‘no’, i.e.
Thank you.
Do you know whether it is possible to use the 5th order polynomial for
angles in Gromacs? I know I can use tables but wish to fit my data into
such a function.
Steven
On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/5/13 8:40 AM, Steven Neumann wrote
Dear Gmx Users,
I created my own CG force field and i process my structure to pdb2gmx. I
process 3 beads I created to check whether the topology is properly created:
Using the CG force field in directory ./CG.ff
No file 'watermodels.dat' found, will not include a water model
Reading
On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:23 AM, Steven Neumann wrote:
Dear Gmx Users,
I created my own CG force field and i process my structure to pdb2gmx. I
process 3 beads I created to check whether the topology is properly
created:
Using
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:42 AM, Justin Lemkul wrote:
On 6/10/13 8:40 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:23 AM, Steven Neumann wrote:
Dear Gmx Users
On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:53 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:42 AM, Justin Lemkul wrote:
On 6/10/13 8:40 AM, Steven Neumann wrote:
On Mon, Jun 10
/13 9:04 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:53 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 8:42 AM, Justin Lemkul wrote:
On 6/10/13 8:40 AM, Steven
On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 9:11 AM, Steven Neumann wrote:
Thank you Justing. Last question - each of my amino acid is one bead. How
can I specify [angles ] between atoms corresponding to different residues?
Shall I add it at the end
On Mon, Jun 10, 2013 at 2:24 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 9:22 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/10/13 9:11 AM, Steven Neumann wrote:
Thank you Justing. Last question - each of my amino acid
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish to set
it up for all atoms with same potential. Is there any example of the table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is
. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
Thanks,
Mohan
On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann s.neuman...@gmail.com
wrote:
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish
or
[ nonbond_params ]
; i j func V(c6) W(c12)
O O 1 0.22617E-02 0.74158E-06
O OA 1 0.22617E-02 0.13807E-05
Or maybe both?
On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/7/13 7:36 AM, Steven Neumann wrote:
Thank you, just getting into this. I just dont understand why
On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/7/13 8:21 AM, Steven Neumann wrote:
Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x) and
it is written that I need to setup parameters C6 and C12. But where I
should specify them
values so the potential will equal zero?
On Fri, Jun 7, 2013 at 2:17 PM, Steven Neumann s.neuman...@gmail.comwrote:
On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/7/13 8:21 AM, Steven Neumann wrote:
Thank you.
Another question... I specify in my table functions
Dear Gmx Users,
I wish to use quartic angle potential and specify all constants. I know it
is a function 6 of [ angles ] but do not know how to place my polynomial
constants?
Thank you,
Steven
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Dear Gmx Users,
I wish to obtain the 2D scatter plot in which I will have my protein
Ca-Ca-Ca tetta angle and the psi angle N(i)-CA(i)-C(k)-N(i+1) of the
central residue?
Would you please help?
Steven
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Dear Gmx Users,
I am building coarse-grained model for my protein. I group them int0 5-10
atoms. I wish to reproduce atomistic equilibrium angles as well as the
spring constant.
Shall I use g_angle -od option and calulate distributions? Then I will use
equilibrium th0 as the centre of the
Dear Gmx Users,
I wish to compare binding free energy obtained from US which I have
sucsessfully conducted and the one obtained using FEP. Would you suggest
any tutorial?
Steven
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* Please
Dear Gmx Users,
I run long simulation of my protein with 50 small molecules in water.
I calculated the RDF (Protein - Water) using -surf mol and -rdf mol_com.
Please, take a look at my plot:
http://speedy.sh/tmJbD/rdf-P-W.png
Could you please, explain me why the second peak is so high? Shall I
Dear Gmx Users,
I produced my trajectory using Gromacs 4.6 on GPUs.
When I try:
trjconv -s md298_gpu.tpr -f md298_gpu.xtc -pbc mol -ur compact -o
md298_gpuURcomp.xtc
Select a group: 0
Selected 0: 'System'
Reading frame 0 time0.000
Precision of md298_gpu.xtc is 0.001 (nm)
Using output
On Mon, Apr 29, 2013 at 10:11 AM, Steven Neumann s.neuman...@gmail.comwrote:
Dear Gmx Users,
I produced my trajectory using Gromacs 4.6 on GPUs.
When I try:
trjconv -s md298_gpu.tpr -f md298_gpu.xtc -pbc mol -ur compact -o
md298_gpuURcomp.xtc
Select a group: 0
Selected 0: 'System
Dear Users,
I am running my puling simulations of ligand with constant velocity. First
I minimize and equilibrate my system:
grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
mdrun -s em.tpr -deffnm em
grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
mdrun -s
Thanks for this. I think option 2 is more reasonable. However, still do not
know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
simulations...
On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier schl...@uni-mainz.dewrote:
Think i now understand your question. Forget what i
Dear Gmx users,
My protien has got some strong acidic and strong basic parts. I fold and
unfold my protein with different temperaturss. I bserved high affinity of
those regions towards each other, they are very close to each other over
the simulation.
How can I possibly check whether my two
Thanks. Which tool would provide me vectors over a time?
Steven
On Thu, Apr 18, 2013 at 8:17 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
Chapter 8 is your friend. Find a tool to feed data to g_analyze.
Mark
On Wed, Apr 17, 2013 at 4:23 PM, Steven Neumann s.neuman...@gmail.com
wrote
Thank you.
Steven
On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/23/13 6:37 AM, Steven Neumann wrote:
Dear Gmx users,
My protien has got some strong acidic and strong basic parts. I fold and
unfold my protein with different temperaturss. I bserved high
Shall I specify one index group for two regions or 2 seprate? g_mindist
asks just for one group.
would twice as cutoff would be sufficent to assess they do not interact?
On Tue, Apr 23, 2013 at 1:54 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you.
Steven
On Tue, Apr 23, 2013
Dear Users,
Does any one know which command is capable to return the vector of a
specified group of 2 atoms (e.g. C=O in protein) over the simulation time?
Steven
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Thanks a lot
Steven
On Tue, Apr 23, 2013 at 2:18 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/23/13 9:15 AM, Steven Neumann wrote:
Shall I specify one index group for two regions or 2 seprate? g_mindist
asks just for one group.
If it only takes one, then you can only give it one
Dear Gmx Users,
Could you please assess my mdp file on GPUs:
title = Protein-ligand complex MD simualation
; Run parameters
integrator = md; leap-frog integrator
nsteps = 1; 200 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress .trr
Dear Users,
Could you advise me please how to calculate vector C-N autocorrelation
function in my protein along the simulation time?
Steven
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, at least, permitting to visualize the plot with xmgrace
without
postprocessing
the .xvg
Francesco
2013/4/16 Mark Abraham mark.j.abra...@gmail.com
On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15/13 12:23 PM, Steven Neumann wrote:
Dear Gmx
I read it... did not know styles are equal to points :)
On Wed, Apr 17, 2013 at 4:08 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/17/13 11:06 AM, Steven Neumann wrote:
What do you mean by style 8?
Did you read trjconv -h? There's an enumerated list in the very
beginning. Mark
, at least, permitting to visualize the plot with xmgrace without
postprocessing
the .xvg
Francesco
2013/4/16 Mark Abraham mark.j.abra...@gmail.com
On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15/13 12:23 PM, Steven Neumann wrote:
Dear Gmx Users,
I
Got this.
Thank you
On Tue, Apr 16, 2013 at 11:21 AM, Justin Lemkul jalem...@vt.edu wrote:
On 4/16/13 5:32 AM, Steven Neumann wrote:
Thank you all.
Would you suggest any link to a script like amb2gmx.pl ? I cannot fina
anything like this - basically I wish to convert top.prmtop
Dear Gmx Users,
I want to calculate a distance matrix of each amino acid (1, 2, ...25)
averaged over simulation time with all amino acids. So matrix of
25x25:
1) is there a tool which can do this or just the use of g_dist fof 600
(25x25 - 25) times?
2) Would you recommend any nice visualisation
On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15/13 9:59 AM, Steven Neumann wrote:
Dear Gmx Users,
I want to calculate a distance matrix of each amino acid (1, 2, ...25)
averaged over simulation time with all amino acids. So matrix of
25x25:
1
On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15/13 10:06 AM, Steven Neumann wrote:
On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15/13 9:59 AM, Steven Neumann wrote:
Dear Gmx Users,
I want to calculate a distance matrix
And another question: I want to analyze all 5 nanoseconds every 20 ns
of my trajectory. Would you suggest using trjcat to create one
trajectory first and then process to g_mdmat or can I specify time
periods (frames) I wish to analyze?
Steven
On Mon, Apr 15, 2013 at 4:08 PM, Steven Neumann
Thank you for this.
Steven
On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15/13 11:08 AM, Steven Neumann wrote:
On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15/13 10:06 AM, Steven Neumann wrote:
On Mon, Apr 15, 2013 at 3:01 PM
). The output
is a symmetrical matrix of smallest distances between all residues.
And nothing else...
Steven
On Mon, Apr 15, 2013 at 4:24 PM, Steven Neumann s.neuman...@gmail.comwrote:
Thank you for this.
Steven
On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15
Dear Gmx Users,
I obtained dcd trajectory from simulation in another software. I wish to
merge many trajectories using trjcat with a proper timestep. Is that option
possible using gromacs or shall use a script to produce tpr file from my
prmtop file e.g. amb2gmx ? Any links for such a script?
Thanks. So in this case no matter what density I will start with e.g.
480 kg/m3 presuming the force filed is correct I should get at given
conditions the density of interest?
Steven
On Mon, Mar 18, 2013 at 10:34 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/18/13 6:14 PM, Steven Neumann wrote
On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/18/13 2:56 PM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to obtain given density for my system for a given molecule
- its a cubic box of 5 nm in dimension.
I calculated that I need 850 molecules to get
. 9 should be ok, since it describes a function of several Fourier
term. I don't understand why grompp propose to chage this to 4...
Baptiste
2013/3/7 Steven Neumann s.neuman...@gmail.com
Dear Gmx Users,
I used charmm server to get the parameters for my new molecule -
alkane. i converted
.
Regards,
Richard
On 13/02/2013 16:07, Steven Neumann s.neuman...@gmail.com wrote:
Dear Gmx Users,
I want to create coarse grained model. I need bond constant and
equilibrium distance according to the equation
V(r) =K (R - Req)^2
I wish to extract bonded potential between beads made out 3 atoms
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