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 pl
Thank you!
Steven
On Thu, Oct 10, 2013 at 3:02 PM, Justin Lemkul 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
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 wrote:
>
>
> On 10/10/13 9:54 AM, Steve
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 wrote:
>
>
> On 10/10/13 9:44 AM, Steven Neumann wrote:
>
>> Thanks. I will place th
Thank you. Would both be equal in terms of gaining computational time?
Steven
On Thu, Oct 10, 2013 at 2:46 PM, Justin Lemkul 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
, 2013 at 2:37 PM, Justin Lemkul 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
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 wrote:
> Thanks a lot.
:
>
>
> 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 pla
onic
> interaction approach, both the CNT 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
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
oms should 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 wrote:
> >
> >
> > On 9/26/1
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 computation
10:20 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
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 wrote:
>
>
> On 9/4/13 10:35 AM, Steven Neumann wrote:
>
>> I am not using any solvent. I mimic the pr
Thanks a lot!
On Wed, Sep 4, 2013 at 3:46 PM, Justin Lemkul 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?
>>
>>
>
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 wrote:
> 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 wrote:
&g
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 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
Thank you! Would you suggest just a cut-off for coulmb?
Steven
On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul 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
&
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 and
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. Woul
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 wrote:
> Thank yo
Thank you a lot!
On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul 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. W
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 wrote:
> They do not dissociate...Are you sure? My mdp specifies o
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
&g
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 att
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]:
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 wrote:
>
>
> On 7/11/13 8:17 AM, Steven Neumann wrote:
>
>> Thank you. Another question: Does RDF depends
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
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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htt
o use 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 wrote:
> Dear All,
>
> Do you know how can I calculate angular distribution of al
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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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 te
same 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
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 grompp
lation. Yet another reason to avoid modifying the C
> code :-)
>
> Mark
>
> On Wed, Jun 19, 2013 at 10:06 AM, Steven Neumann
> wrote:
> > I will speak to someone who is familiar with the code. However, my
> Gromacs
> > version is installed on the cluster, can I crea
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 wrote:
>
>
>
> On Tue, Jun 18, 201
On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham wrote:
> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann >wrote:
>
> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul wrote:
> >
> > >
> > >
> > > On 6/10/13 5:16 AM, Steven Neumann wrote:
> >
On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul 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 m
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 wrote:
>
>
> On 6/12/13 10:01 AM, Steven Neumann wrote:
>
>> Dear Gmx Us
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
So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions
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* Please don't pos
60 types of atoms and 60 atoms in total belonging to one residue
On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham wrote:
> How many atom *types* are there?
>
>
> On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann >wrote:
>
> > and 1830 1-4 interactions... there are "57
and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"
On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann wrote:
> "All possible interactions = 60*60/2 = 1800. Where grompp takes another 30
> from?
>
>
> On Wed, Jun 12, 2013 at 12:52 PM, Mark Abra
offs... grompp is not doing
> a neighbor search!
>
> Mark
>
>
> On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann >wrote:
>
> > On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham > >wrote:
> >
> > > grompp is just enumerating the possible combinations
;
> Mark
I understand...but why for 60 mer polypeptide there are 1830 nonbonded
interactions ?
>
>
> On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann >wrote:
>
> > I got it. However,
> >
> > I have 60 atoms in my chain all with given C6 and C12 with a combination
&g
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 wrote:
> I got it. However,
>
> I have 60 at
Number of degrees 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,
On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul 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
>> potenti
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 wrote:
>
>
> On 6/12/13 5:30 AM, 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 force
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 wrote:
>
>
> On 6/11/13 4:12 PM, Steven Neumann wrote:
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.
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 wrote:
>
>
> On 6/11/13 10:46 AM, Steven Neumann wrote:
>
>> I was not sure
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 >wrote:
>
> > Dear Gmx Users,
> >
> > I am running CG simulation and I wish my beads
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
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul 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 wrote:
>>>
>>>
>>
On Mon, Jun 10, 2013 at 2:24 PM, Justin Lemkul wrote:
>
>
> On 6/10/13 9:22 AM, Steven Neumann wrote:
>
>> On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul wrote:
>>
>>
>>>
>>> On 6/10/13 9:11 AM, Steven Neumann wrote:
>>>
>>> Th
On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul 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?
>> S
3 9:04 AM, Steven Neumann wrote:
>
>> On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul wrote:
>>
>>
>>>
>>> On 6/10/13 8:53 AM, Steven Neumann wrote:
>>>
>>> On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul wrote:
>>>>
>>>>
On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul wrote:
>
>
> On 6/10/13 8:53 AM, Steven Neumann wrote:
>
>> On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul wrote:
>>
>>
>>>
>>> On 6/10/13 8:42 AM, Justin Lemkul wrote:
>>>
>>>
>
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul 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 wrote:
>>>
>>>
>>
On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul 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
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 60central_C
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 wrote:
>
>
> On 6/5/13 8:40 AM, Steven Neumann wrote:
>
values so the potential will equal zero?
On Fri, Jun 7, 2013 at 2:17 PM, Steven Neumann wrote:
>
>
>
> On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul wrote:
>
>>
>>
>> On 6/7/13 8:21 AM, Steven Neumann wrote:
>>
>>> Thank you.
>>> Another ques
On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul 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 wher
[ 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 wrote:
>
>
> On 6/7/13 7:36 AM, Steven Neumann wrote:
>
>> Thank you, just getting into this. I just dont underst
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 >wrote:
>
> > Dear Gmx Users,
> >
> > I want to specify a table to mdrun for non bond
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 t
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 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 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 gaussian
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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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 u
On Mon, Apr 29, 2013 at 10:11 AM, Steven Neumann wrote:
> 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
> Select
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 p
Thanks anyway. I will try tu pull it 20-40 times to tell something.
Steven
On Fri, Apr 26, 2013 at 1:23 PM, Thomas Schlesier wrote:
> Don't know. One idea i have: Take a flexible and a relative rigid system
> and perform simulations with the same starting conditions (-> using -t
> *.cpt). I woul
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 wrote:
> Think i now understand your question. Forget what i wrote before.
> I cou
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 nvt2
Thanks a lot
Steven
On Tue, Apr 23, 2013 at 2:18 PM, Justin Lemkul 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 t
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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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 wrote:
> Thank you.
>
> Steven
>
>
> On Tue, Apr 23, 2013
Thank you.
Steven
On Tue, Apr 23, 2013 at 1:23 PM, Justin Lemkul 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 w
Thanks. Which tool would provide me vectors over a time?
Steven
On Thu, Apr 18, 2013 at 8:17 PM, Mark Abraham wrote:
> 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 >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 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 regi
I read it... did not know styles are equal to points :)
On Wed, Apr 17, 2013 at 4:08 PM, Justin Lemkul 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
d, but it could be more useful using as x the
> frame
> > number.
> > This could, at least, permitting to visualize the plot with xmgrace
> without
> > postprocessing
> > the .xvg
> >
> >
> >
> > Francesco
> >
> >
> > 2013
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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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
Got this.
Thank you
On Tue, Apr 16, 2013 at 11:21 AM, Justin Lemkul 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 w
s could, at least, permitting to visualize the plot with xmgrace without
> postprocessing
> the .xvg
>
>
>
> Francesco
>
>
> 2013/4/16 Mark Abraham
>
> > On Apr 15, 2013 6:27 PM, "Justin Lemkul" wrote:
> > >
> > >
> > >
&g
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?
tha
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 wrote:
> Thank you for this.
>
> Steven
>
> On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul wrote:
> >
> >
>
Thank you for this.
Steven
On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul wrote:
>
>
> On 4/15/13 11:08 AM, Steven Neumann wrote:
>>
>> On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul wrote:
>>>
>>>
>>>
>>> On 4/15/13 10:06 AM, Steven N
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
On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul wrote:
>
>
> On 4/15/13 10:06 AM, Steven Neumann wrote:
>>
>> On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul wrote:
>>>
>>>
>>>
>>> On 4/15/13 9:59 AM, Steven Neumann wrote:
>>>&g
On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul 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. S
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 t
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 wrote:
>
>
> On 3/18/13 6:14 PM, Steven Neumann wrote:
On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul 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.
>>
>
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