Hello,
I am sorry those were two different questions.. I wanted to know what
this statement actually mean?
The set pressure should reflect whatever system you are trying to model.
Thank you
With Regards
Kavya
I don't see the connection to my comment about pressure, but I'll address
this
.. I
may
be able to get some rough estimate of pressure..
So I wanted to simulate this protein at a temperature near 90 or 100 deg C.
Thank you
With Regards
Kavya
On Mon, Oct 17, 2011 at 8:45 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Hello,
I am sorry those were two
I dont know the details but this link may be useful.
http://code.google.com/p/acpype/
Kavya
On Sat, Oct 15, 2011 at 2:01 PM, leila karami karami.lei...@gmail.comwrote:
Dear gromacs users
I want to do MD simulation of protein-ligand.
I read a tutorial by John E. Kerrigan Tutorial for
such clashes if at all
in vmd? I am using dodecahedron box. can it be visualised as it is in vmd?
Thank you
With regards
Kavya
On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M hmkv...@gmail.com wrote:
Thanks.
On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote
Dear users,
I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the
Thanks.
On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear users,
I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using
Dear users,
I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the
Its strange I get some mails, But Dr. Mark's reply for
my previous mail I dint get. So I thought there is some
problem.
Thank you
With Regards
Kavya
On Thu, Aug 18, 2011 at 9:24 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Respected Sir,
I am not receiving reply mails
Dear users,
While calculating the box dimensions during a simulation
of 20ns I got some strange values of the averages -
Command used:
g_energy -f ener.edr -o box.xvg
Output:
Energy Average Err.Est. RMSD Tot-Drift
On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
While calculating the box dimensions during a simulation
of 20ns I got some strange values of the averages -
Command used:
g_energy -f ener.edr -o box.xvg
Output:
Energy
4.5.3 and
4.5.4 versions. Sorry I sent the mail twice as I did not receive
Dr. Mark's reply form the forum.
Thank you
With Regards
Kavya
On Wed, Aug 17, 2011 at 4:15 PM, Kavyashree M hmkv...@gmail.com wrote:
Sorry Sir,
I did not get that mail from the forum.
Thank you
With Regards
Kavya
Respected Sir,
I am not receiving reply mails to my gmail id, even
when it is answered. Kindly check Sir.
Thank you
With Regards
M. Kavyashree
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear users,
While calculating the box dimensions during a simulation
of 20ns I got some strange values of the averages -
Command used:
g_energy -f ener.edr -o box.xvg
Output:
Energy Average Err.Est. RMSD Tot-Drift
Dear users,
I have done some 16 simulations of a protein with mutations,
by keeping the distance between protein atom and the simulation
box to be 1.0nm (i.e, -d option in editconf) but only in one of the
simulation I found violation of minimum image distance. So Should
I increase the box size
hope my i am putting the question clearly.
Thank you
with regards
Kavya
On Fri, Aug 12, 2011 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear users,
I have done some 16 simulations of a protein with mutations,
by keeping the distance between protein atom
Dear gromacs users,
I wanted to know the steps to be followed
in order to generate a topology for a new
ligand. I went through the mailing list and
http://www.gromacs.org/Documentation/How-tos/Parameterization
but was not clear.
Awaiting your suggestions
Thanking you
With regards
M. Kavyashree
suggestions.
Thank you
With Regards
M. Kavyashree
On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear gromacs users,
I wanted to know the steps to be followed
in order to generate a topology for a new
ligand. I went through the mailing list
ragotha...@gmail.com
wrote:
Look at this paper where the simulation was done on a protein dimer:
http://www.ncbi.nlm.nih.gov/pubmed/17027497
On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 18/07/2011 3:08 PM, Kavyashree M wrote:
Dear users,
I am working
, and depends on what
your hypothesis is.
Ragothaman
On Mon, Jul 18, 2011 at 7:49 AM, Kavyashree M hmkv...@gmail.com wrote:
Thank you Sir,
The interface is connected by salt bridges and hydrogen bonding
interactions and not severely
hydrophobic. I tried simulating the monomers it stayed
Dear users,
I am working on a protein which is a dimer (in the crystal structure),
predicted according top PISA.
and some of the homologous proteins are dimers (covalent /non-covalent) some
are monomers.
There has not been any literature regarding the fact that the functional
unit is a dimer, ie
Dear users,
I was trying to run gromacs-4.5.3 in IBMcluster using mpich-1.2.7
rather than openmpi. But I was getting some error. Sorry I donot
remember the error. But Is it possible to run gromacs-4.5.3 using
mpich implementation?
Thank you
With Regards
M. Kavyashree
--
gmx-users mailing list
On Tue, Jul 12, 2011 at 10:15 PM, lina lina.lastn...@gmail.com wrote:
On Wed, Jul 13, 2011 at 12:21 AM, Justin A. Lemkul jalem...@vt.edu
wrote:
Kavyashree M wrote:
Dear users,
I was trying to run gromacs-4.5.3 in IBMcluster using mpich-1.2.7
rather than openmpi. But I was getting
Dear users,
Has anyone done simulation with a broken crystal structure?
I know that it can be modeled before simulating. But I just wanted
to know whether any one had done with the crystal structure having
breakage as such without modelling.
Thanking you
Respectfully
M. Kavyashree
--
gmx-users
Sir,
Ok Thanks.
With Regards
M. Kavyashree
On Tue, Jun 28, 2011 at 4:25 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear users,
Has anyone done simulation with a broken crystal structure?
I know that it can be modeled before simulating. But I just wanted
to know
Dear Sir
Thanks I got the point!
Thanking you
With Regards
M. Kavyashree
On Mon, Jun 27, 2011 at 12:19 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi Kavya,
I did use dodecahedron cell. but how does using a dodecahedron cell
be advantageous than any other cell when minimum image
Dear users,
I apologize for asking the same question. but I wanted a clarification
regarding this
I had done a simulation for 100ns which had minimum image violation
after 27ns. I have asked this question several times and people have
suggested me not to use the results. But I just wanted to
Sir,
I would like to thank you for patiently replying for my repeatedly asked
question.
For most stable, well-behaved proteins, setting a suitable box size at the
outset of the simulation is sufficient to avoid spurious PBC interactions.
In your case, there are several possibilities: (1)
Dear Sir,
I did use dodecahedron cell.
On Mon, Jun 27, 2011 at 12:35 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hey,
Maybe I missed this, but what type of unit cell did you use? You
should use a rhombic dodecahedron.
I did use dodecahedron cell. but how does using a dodecahedron cell
Dear users,
Any suggestions?
Thank you
M. Kavyashree
On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
In one of the simulations while calculating box dimensions
using g_energy this output was obtained -
Statistics over 5001 steps [ 0. through
. Kavyashree
On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear users,
Any suggestions?
You haven't provided nearly enough diagnostic information for anyone to
offer you any useful help (as Mark said yesterday). For example, please
provide:
1
Sir,
I tried it already but It was huge file. this kind of nan comes only
for RMSD not for any other term. I will try looking into that file again.
Thanks
With regards
M. Kavyashree
On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Sir,
I am
:53 PM, Kavyashree M hmkv...@gmail.com wrote:
Sir,
I tried it already but It was huge file. this kind of nan comes only
for RMSD not for any other term. I will try looking into that file again.
Thanks
With regards
M. Kavyashree
On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem
the
box dimensions for the whole trajectory for eg.
Box-X most of the time has value around 9. very
few times it gets a value near 8.9..
Thank you
With Regards
M. Kavyashree
On Fri, Jun 24, 2011 at 6:18 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Sir,
I tried it already
24, 2011 at 6:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Sir,
I went through the whole .edr file for one
specific term in which I was getting nan.
Of the three columns (Energy; Av. Energy; Sum Energy)
order (power) for temperature did not change at all
Dear user,
When projection of a trajectory (50ns) on an eigen vector
was visualised in pymol, there was broken chains, but when
I projected the simulation (continued for 50 more ns ie.,
total 100ns) this broken chain was not seen why?
Thanking you
With Regards
M. Kavyashree
--
gmx-users mailing
at 1:56 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Did you make the molecules whole and removed jumps (in case of a multimer)
prior to filtering?
Cheers,
Tsjerk
On Jun 24, 2011 8:10 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear user,
When projection of a trajectory (50ns) on an eigen
. Then it should not be a problem.
Best Wishes,
Sarath
Did you make the molecules whole and removed jumps (in case of a
multimer)
prior to filtering?
Cheers,
Tsjerk
On Jun 24, 2011 8:10 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear user,
When projection of a trajectory
On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I did ED analysis for one of the trajectories,
when I visualised the trajectory along the first
five eigen vectors using g_nmtraj it does not
show much movements. It was a simulation of
100 ns.
My doubt
Thank you Sir!
With regards
M. Kavyashree
On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
trjconv -fit rot+trans
Cheers,
Tsjerk
On Jun 23, 2011 8:12 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear Users,
Are there any tool for superposing the trajectory
. Kavyashree
On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M hmkv...@gmail.com wrote:
Thank you Sir!
With regards
M. Kavyashree
On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
trjconv -fit rot+trans
Cheers,
Tsjerk
On Jun 23, 2011 8:12 AM, Kavyashree M hmkv
it, we should at least know
exactly what you've tried. Copy-paste the commands exactly as you
issued them, and provide the parts of the output that seem relevant.
Cheers,
Tsjerk
On Thu, Jun 23, 2011 at 9:54 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear Sir,
I tried fitting the proteins
On Thu, Jun 23, 2011 at 10:56 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear Sir,
1 simulation for 100ns -
ED analysis proceeded as follows:
g_covar -s input.tpr -f .input.xtc -o eigenvectors.xvg -v
eigenvalues.trr -xpma covar.xpm
g_anaeig -s input.tpr -f input.xtc -v eigenvectors.trr
Dear users,
I did ED analysis for one of the trajectories,
when I visualised the trajectory along the first
five eigen vectors using g_nmtraj it does not
show much movements. It was a simulation of
100 ns.
My doubt is when I visualise the trajectory in
pymol calculated just after simulation I
Dear users,
In one of the simulations while calculating box dimensions
using g_energy this output was obtained -
Statistics over 5001 steps [ 0. through 10. ps ], 3 data
sets
All statistics are over 1978700 points
Energy Average Err.Est. RMSD
Dear users,
When are checking the cosine content of a PC, (Pls. Correct me if I am
wrong)
This is the command we use -
g_analyze -f input-principle-component.xvg -cc outputcosine
content.xvg
and for first PC output says -
Cosine content of set 1 with 0.5 periods: ---
for nth PC also it says
Dear users,
I ran 100ns simulation for 4 proteins, 3 of them were
non covalent dimers in solution, but only 1 is a covalent
dimer connected by a disulphide bridge. I used monomers
to run the job.
Only in the case of covalent dimer I was getting severe
minimum image violation ie. out of
, 2011 at 2:46 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear users,
I ran 100ns simulation for 4 proteins, 3 of them were
non covalent dimers in solution, but only 1 is a covalent
dimer connected by a disulphide bridge. I used monomers
to run the job.
Only
Dear users,
In one of the simulations I have run, I have transfered
it from one system to another so some data points were missing
what I should do now. how to find which data points are missing?
Thank you
With regards
M. Kavyashree
--
gmx-users mailing listgmx-users@gromacs.org
)
an number of data points is only 1978700 compared to actual data points
of 501. where could be the error? and is it possible to get the missing
data
points?
Thanks
With regards
M. Kavyashree
On Tue, Jun 14, 2011 at 11:54 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
In one
Dear users,
While analyzing an MD simulation run for 100ns, for temperature,
pressure, volume and density, I got an output like this -
Energy Average Err.Est. RMSD Tot-Drift
---
Dear Sir,
g_mindist analysis showed the violation of minimum image convention, it
was violated over a short period of time and then it came back to normal.
I attach the plot herewith. Should this data be discarded or any useful
information
can be obtained.
Thank you
With Regards
M. Kavyashree
Dear users,
I have some basic doubts regarding analysis of data:
1. Can the .xtc file from MD be used directly for analysis
without applying -pbc nojump or mol option? [I had
asked the same question before but was not clear
with the answer.
2. While calculating the RMSIP
Dear Sir,
Thank you sir for the clarification. But if there is only one
polymer (protein) with water in the system then also is it
necessary because in one of the mails -
http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html
there was a discussion regarding this topic. So I
Dear Sir,
Thanks for your patient reply Sir.
With Regards
M. Kavyashree
On Sat, Jun 11, 2011 at 9:57 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Kavya,
It is absolutely necessary that the molecules be whole, and in the
case of multimers, correctly assembled.
But if there is
Dear Sir,
Thank you Sir for the clarification.
Need to explore about this.
Thanking you
With Regards
M. Kavyashree
On Wed, Jun 8, 2011 at 2:35 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Kavya,
Thanks sir. I will go through them. However I have referred -
A Tutorial on Principle
Dear Sir,
Ok Sir thanks.
Thanking you
With Regards
M. Kavyashree
On Tue, Jun 7, 2011 at 10:47 AM, Ran Friedman ran.fried...@lnu.se wrote:
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx-users] Essential dynamics - concepts
To: Discussion list for GROMACS users
Dear Sir,
Thanks for giving a clearer picture about essential dynamics. I was very
eagerly awaiting for a reply. Thanks you very much :).
No, ED does not make any assumptions on the nature of motions. It does
not distinguish anharmonic from harmonic motions. It also does not
distinguish
Dear Sir,
Thanks sir. I will go through them. However I have referred -
A Tutorial on Principle component Analysis by Lindsay I Smith.
Which gave a good understanding about the concepts. Still I
have some doubts regarding eigen values, as you have told
I will think over them again.
But one
Dear Gromacs users,
I am new to essential dynamics, I have gone through
some fundamentals in PCS, the mailing list related to ED
and few publications by -
Amadei (Proteins, 17, 412-425, 1993),
a. Amadei (journal of biomolecular structure and dynamics, 13, 615, 1996)
b. Berk Hess (Physical
-- Forwarded message --
From: Mark Abraham mark.abra...@anu.edu.au
Date: Fri, Jun 3, 2011 at 12:58 PM
Subject: Re: [gmx-users] option -pbc in trjconv
To: Discussion list for GROMACS users gmx-users@gromacs.org
On 3/06/2011 3:42 PM, Kavyashree M wrote:
Dear users,
I wanted
Dear users,
I wanted to ensure that the option of -pbc in trjconv is only for
visualization,
and if I do all possible calculations with the original .xtc file there wont
be any
problem.
Thank you
With regards
M. Kavyashree
--
gmx-users mailing listgmx-users@gromacs.org
Dear users,
I was using g_covar (gmx 4.5.3) to find the eigenvalue and
eigenvectors. When I used for protein which is actually - 3740 in
number, it gave a total of 11220 eigenvalues, similarly for bacbone,
c-alpha atoms, the number of eigenvalues given was not matching
with the number of
, 2011 at 2:44 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I was using g_covar (gmx 4.5.3) to find the eigenvalue and
eigenvectors. When I used for protein which is actually - 3740 in
number, it gave a total of 11220 eigenvalues, similarly for bacbone,
c-alpha atoms
will this effect the results of the
simulations?
Kindly let me know whether I need to redo the simulation again? or is there
any way to correct this or can it be ignored?
Thanking you
With regards
M. Kavyashree
On Mon, May 30, 2011 at 10:36 AM, Kavyashree M hmkv...@gmail.com wrote:
Hello sir
30, 2011 at 12:24 PM, Kavyashree M hmkv...@gmail.com wrote:
Hello Sir,
The difference between the rcolumb (1.4nm) and minimum image distance
that was obtained between two hydrogen HZ2 and HZ3 atoms of 2 lysine
residues (1.39714nm) is 0.00286nm = 0.0286Ang,
Since this distance is smaller
Hello sir,
I had used a dodecahedron cell for simulation. I have run
the simulation for 100ns, did you man I have to restart the
simulation again?
Thanking you
Kavya
On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Kavya,
shortest periodic distance is 1.39714
Hello Sir,
I saw the 21824th frame, it dint look unusually stretched when
I superposed against the initial pdb file. there atoms were hydrogen
atoms of two lysine residues.. And in the entire strttch of 100ns simulation
this is the only periodic image interaction observed, Is it possible to
Dear users,
I ran a simulation of a protein in water with rlist = rcoloumb = 1.4nm,
rvdw = 1.0nm, with PME and the distance between in the periodic
was set to a minimum of 2.0 i.,e distance between protein and cell
edge was set to 1.0nm, Even then, when I ran g_mindist, there was
a message
Dear users,
I was running an MD in a system with 8 cores, for some
reasons I had to shift the job to another system with
same OS and gromacs version. After I started runnning
it said
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not
Dear users,
I was running an MD in a machine with 2 quad core processors
using all 8 cores system cores, for some reasons I had to shift the
job to another machine with 2 quad cores processors, identical OS
and gromacs version using 8 cores. After I started runnning using check
point
file
Respected Sir,
So that number doesnt mean what it says!
Thanking you
With regards
kavya
On Wed, May 11, 2011 at 4:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 11/05/11, *Kavyashree M * hmkv...@gmail.com wrote:
Dear users,
I was running an MD in a machine with 2 quad core
Dear users,
I wanted to know when DEFINE = -DFLEXIBLE has to be used.
its given in the manual that it has to be used when we require flexible
water instead of rigid waters, so if I am using tip4p water model and
OPLSAA force field, and i use DFLEXIBLE option in EM and not in
position MD, is
Thanks
With Regards
Kavya
On Tue, May 10, 2011 at 5:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear users,
I wanted to know when DEFINE = -DFLEXIBLE has to be used.
its given in the manual that it has to be used when we require flexible
water instead
Dear gromacs users,
While doing energy minimization for a protein (from pdb), with oplsaa force
field
and tip4p water model, there was an error and em stopped -
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well
Ok thanks
On Fri, Apr 15, 2011 at 9:56 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear gromacs users,
While doing energy minimization for a protein (from pdb), with oplsaa
force field
and tip4p water model, there was an error and em stopped -
Fatal error
Dear gromacs users,
I am trying to simulate a 225aa protein at 300K in water,
with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during
position restrained md.
integrator = md
dt = 0.002
nsteps =
:
Kavyashree M wrote:
Dear gromacs users,
I am trying to simulate a 225aa protein at 300K in water,
with OPLSAA force filed, tip4p water model, using the
parameters below (for pressure equilibration) during
You're not doing NPT. You haven't specified pcoupl or any of the other
relevant parameters
The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc). or is this value tolerable?
On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M
Ok Thanks.
On Wed, Apr 13, 2011 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983)
stated a density of 0.999g/cc at 298K and 1atm, which is nowhere
close to the value i have got. (1.025g/cc
mark.abra...@anu.edu.auwrote:
On 16/03/11, *Kavyashree M * hmkv...@gmail.com wrote:
Dear users,
Upon was trying to simulate an npt ensemble (protein in water),
pressure was coupled using parinello rahman system with tau_p = 2,
tau_t = 1; compressibility 4.5e-5, type = isotropic.
(cut off
:
Kavyashree M wrote:
Thank you Sir
I am using OPLSAA with tip4p water model, I agree to the fact that
it will oscillate but the oscillation is this case was from appr. -1000bar
to 1000bar. And as it is stated in the FAQ regarding the variation of
fluctuations with number of waters
Thank you Justin!
On Wed, Mar 16, 2011 at 9:28 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Thank you Justin,
When I went through most of the mailing list the fluctuations are not so
high
and even in the FAQ it was mentioned in the range of 500-600 bar for 216
Dear users,
Upon was trying to simulate an npt ensemble (protein in water),
pressure was coupled using parinello rahman system with tau_p = 2,
tau_t = 1; compressibility 4.5e-5, type = isotropic.
(cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9;
rcoulomb = 1.2; rlist = 1.2).
Dear users,
What is the difference between densities predicted by tip4p and spc
models?
I am using tip4p (with OPLSAA forcefield) in the simulation, during position
restrained
dynamics, Average water density is around 1015kg-m-3 at 300K which is quite
far from
expt value..
The Dispersion
Dear users,
Which temperature coupling scheme is recommended during
equilibration? and do we have to use the same scheme for
production MD also?
Thanking you
With Regards
M. Kavyashree
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Thank you sir for the reply!
On Mon, Mar 7, 2011 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear users,
Which temperature coupling scheme is recommended during
equilibration? and do we have to use the same scheme for
Theoretically, any of them. Nose
On Sat, Mar 5, 2011 at 12:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Assessing equilibration of an observable requires observing for a great
deal longer than the time scale of the intrinsic variability of that
observable. Only then can you assess whether any change in the value of
Dear gromacs users,
1. When one is using OPLSAA force field for simulation a protein of say
100aa to 250aa long protein, TIP4P water model in gromacs 4.5.3
what are the values of cut offs to be used ie., rcoloumb, rvdw,
rvdw-switch and rlist? I have gone through the manual and papers and
Dear gromacs users,
1. When one is using OPLSAA force field for simulation a protein of say
100aa to 250aa long protein, TIP4P water model in gromacs 4.5.3
what are the values of cut offs to be used ie., rcoloumb, rvdw,
rvdw-switch and rlist? I have gone through the manual and papers and
On Sat, Mar 5, 2011 at 12:22 AM, Justin A. Lemkul jalem...@vt.edu wrote:
It is difficult to say for certain how OPLS should be used with MD, since
it was originally designed for different software doing MC simulations. I
commonly see rlist=rcoulomb=rvdw=1.0 with vdwtype = cutoff and
mutation or cysteine mutation.
I finalised on the value of rlist = rcolomb = 1.35nm so as not to take
risk.
is that fine?
Thank you
M. Kavyashree
On Sat, Jan 22, 2011 at 6:26 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Sir,
System is a protein with 123 aa
22, 2011 at 6:41 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Sir,
Yes sir I am using PME. And one more thing I noticed was, the protein
has
7 disulphide bonds, so when I reduce all the cystine to cysteine or to
alanine,
the the sum of charge group radii reduces
the preference of vdw_type (cutoff/shift or
switch),
Thank you
MKS
On Sat, Jan 22, 2011 at 11:18 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
I went through few papers related to OPLS-AA, but could not find
any specific values mentioned for vdw and coulomb intecations
, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear gromacs users,
I am using gromacs 4.5.3, OPLSAA force field, and the cut off
parameters
are as shown below
jalem...@vt.edu wrote:
Kavyashree M wrote:
Sir,
What exactly can be wrong with the topology? As I tried with
I don't know, what's in your system? Was the topology created entirely by
pdb2gmx, or have you introduced some other molecules that you've
parameterized?
different PDBs
Dear gromacs users,
while using grompp I got a message :
System has non-zero total charge: -9.98e-01
This is non integral charges. What should I add using genion?
+1 charge? Why am I getting such non integral charges?
I also checked for any breakage in the chain and found no such
ends.
Thank you Sir!
With Regards
MKS
On Mon, Jan 17, 2011 at 5:37 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear gromacs users,
while using grompp I got a message :
System has non-zero total charge: -9.98e-01
This is non integral charges. What should I add using
Dear Gromacs users,
I wanted to know whether it is correct doing minimization
in double precision and rest all - pdb2gmx, editconf, genbox,
grompp and mdrun itself in single precision.
I had got convergence during energy minimization using double
precision but not single precision (input
Dear Gromacs users,
I am new to gromacs. I want to simulate a system
(protein) with a dodecahedron box in order to minimize
the time.
rlist = rcolumb = 1.2nm; (PME)
rvdw = 1.1nm; rvdw_switch = 0 (using vdwtype = switch)
so while setting the simulation box, should i give the
Thank you Tsjerk for your suggestions!
So according to this my minimal box size should be
0.6nm in order to avoid PBS effects and due to the
water effects i have to set it 1nm or higher.
So this rule is irrespective of the box type we choose
isnt it?
I got the clue for my second question.
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