Dear,
when i make MD of my system, i set the MD stop ater 3ns. however, when the
gromacs stop , i find that the system of protein and ligand is not equilibrium,
i want to continue the process to 5ns. but i don't konw how to do this.please
help me.
thank you very much!
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gmx-users mailing
Dear Justin,
Thanks for your immediate reply.
Is it possible to do clustering based on side-chain RMSF in gromacs?
What about dihedral angle order parameters in gromacs?. Does it provide any
information about what I want to know?
Thanking you once again
regards
Anu
On Mon, Apr 1, 2013 at
IIRC, the default Cygwin gcc is too old to compile GROMACS, as discussed on
this list in the last few months some time. I don't know how easy it is to
get a new one via the Cygwin package system.
Mark
On Mon, Apr 1, 2013 at 5:03 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 1, 2013 at
Sorry, meant to post this on the bb.
Gesendet:Dienstag, 02. April 2013 um 11:50 Uhr
Von:lloyd riggs lloyd.ri...@gmx.ch
An:vvcha...@gmail.com
Betreff:Aw: Re: [gmx-users] Re: density profile
How would you set up a gas/gas interface, say modeled after a large gas planet or upper
Dear Users,
I have inserted protein and carbohydrate in DPPC membrane according to the
KALP
tutorials. After inserting both molecules, I checked by using VMD, the atoms
around my protein and ligand were overlapped. But I applied position
restraints to protein and ligand and run
Inflategro
Dear All!
I have a doubt about the rightness of ligand/molecule integration in the
topology file. I'm using an amber (tleap) or swissparam.ch to build a
topology of the residue (modified trna). Is it neccessary to generate a
position restrain file (genrestr program) for this residue or not? I've
On 4/2/13 3:24 AM, aixintiankong wrote:
Dear,
when i make MD of my system, i set the MD stop ater 3ns. however, when the
gromacs stop , i find that the system of protein and ligand is not equilibrium,
i want to continue the process to 5ns. but i don't konw how to do this.please
help me.
On 4/2/13 4:58 AM, anu chandra wrote:
Dear Justin,
Thanks for your immediate reply.
Is it possible to do clustering based on side-chain RMSF in gromacs?
Not that I'm aware of.
What about dihedral angle order parameters in gromacs?. Does it provide any
information about what I want to
On 4/2/13 5:56 AM, sdshine wrote:
Dear Users,
I have inserted protein and carbohydrate in DPPC membrane according to the
KALP
tutorials. After inserting both molecules, I checked by using VMD, the atoms
around my protein and ligand were overlapped. But I applied position
restraints to protein
On 4/2/13 6:07 AM, alex rayevsky wrote:
Dear All!
I have a doubt about the rightness of ligand/molecule integration in the
topology file. I'm using an amber (tleap) or swissparam.ch to build a
topology of the residue (modified trna). Is it neccessary to generate a
position restrain file
On 01.04.2013 14:58, 라지브간디 wrote:
I tried to install 4.6.1 version through cygwin and got following error by
using this command :
In the last weeks of March 2013, there has been significant
progress made on the cygwin packages. Since April, 1st, there
is even a 64-bit build including gcc 4.8
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I thoroughly search the Mailing-list Archive for the REMD problem.
It was a really helpful to start.
My system consist of peptide + water.
I used the
On 4/2/13 7:13 AM, rama david wrote:
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I thoroughly search the Mailing-list Archive for the REMD problem.
It was a really helpful to start.
My
On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 7:13 AM, rama david wrote:
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I thoroughly search the Mailing-list
Dear users,
Kindly clarify my doubt regarding salt bridge calculation.
Thank you
Regards
Kavya
On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
For calculating salt bridge in proteins I
am using g_hbond instead of g_saltbr.
In g_hbond I use contact and
I would look on some paper which temperature ranges and conditions
(NPT/NVT) were used for systems of a similar size and with a similar aim.
2013/4/2 rama david ramadavidgr...@gmail.com
Dear friends ,
Thank you justin and Mark for your suggestion
I increases my temp range from 310-360 K
Thank you Massimo sandal, Justin and mark ,
I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive in REMD .
So I want to conform protocol from the Expert and experience person )
I will be grateful to you for your suggestion.
On Tue, Apr 2, 2013 at
hello gromacs users,
I was trying to install gromacs 4.5.5 on the cluster.
the cluster info:
uname -a
Linux mgr.itp 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT 2007 x86_64
x86_64 x86_64 GNU/Linux
I have successfully installed fftw3 and gsl on it.
then I try to install the Gromacs 4.5.5
You can use g_dist with specific atoms indices to calculate distances,
if you already have the information about atoms involved in salt
bridge interactions.
On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
Kindly clarify my doubt regarding salt bridge
Hello:
I am wondering is double precision supported in current 4.6.1 GPU
version? Otherwise it would be very slow to use CPU version running free
energy calculations
thank you very much
best
Albert
--
gmx-users mailing listgmx-users@gromacs.org
On Apr 2, 2013, at 5:47 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I am wondering is double precision supported in current 4.6.1 GPU version?
Otherwise it would be very slow to use CPU version running free energy
calculations….
Hi Albert,
no, GPU calculations can be done only in
Dear all,
I am trying to get the density profile for my liquid-vacuum interface using
g_density -f trr -s tpr however g_density gives Segmentation fault. Does
anyone had clue what could be wrong? Please comment, Thanks.
Group 0 ( System) has XXX elements
Group 1 (
Sir,
Thank you very much for your reply. I wanted to calculate
Salt bridge in the whole protein so i am not mentioning the
residues involved. The problem with g_saltbr was that if I
have to calculate the accessibility of these atoms it will be
a problem because it gives the charge groups but not
On 4/2/13 7:38 AM, Erik Marklund wrote:
On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 7:13 AM, rama david wrote:
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I
On 4/2/13 9:24 AM, rama david wrote:
Thank you Massimo sandal, Justin and mark ,
I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive in REMD .
So I want to conform protocol from the Expert and experience person )
I will be grateful to you for your
On 4/2/13 11:58 AM, Kavyashree M wrote:
Sir,
Thank you very much for your reply. I wanted to calculate
Salt bridge in the whole protein so i am not mentioning the
residues involved. The problem with g_saltbr was that if I
have to calculate the accessibility of these atoms it will be
a problem
On 4/2/13 11:57 AM, Elisabeth wrote:
Dear all,
I am trying to get the density profile for my liquid-vacuum interface using
g_density -f trr -s tpr however g_density gives Segmentation fault. Does
anyone had clue what could be wrong? Please comment, Thanks.
Group 0 ( System) has
Hi Michael,
Do the codes now support walking in multidimensional parameter space? i.e.,
a state is defined by a set of lambda parameters {l1,l2,l3,...,ln} and a MC
move is attempted along one of the parameter, which is randomly picked.
Thanks,
Dejun
--
View this message in context:
Hi Justin,
Do I have to read less frames to circumvent the problem? I know g_density
has been used for this purpose so there should be a way to resolve this. I
am reading 1000 frames...
Thanks
On 2 April 2013 12:40, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 11:57 AM, Elisabeth wrote:
Thank you justin.
I will do the same.
On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 9:24 AM, rama david wrote:
Thank you Massimo sandal, Justin and mark ,
I also goes through the article and GMX archive.
But I confuse with the protocol ( I am naive in
Hi again!
Just a quick update - we've had lots of interest for the webinar this thursday
(which is great!).
We're pretty close to breaking their all-time record for webinars, and you
still have two days to sign up, so hopefully we'll do it ;-)
I will try to answer as many Gromacs/GPU-related
Hi, Dejun-
Right now, the vector of lambda parameters is simply vdw, coul, bonded,
restraint, temperature. You can't have, say, 2 different coul vectors or
two different restraint vectors for different restraints. But you can
change any of these components.
You define the vector manually by
Sir,
This g_hbond will generate a matrix similar to
what g_saltbr would have given in terms of variation
of distance between two charge groups.
I want to find out the variation of all the salt bridges
in the protein over the trajectory, if I have to use g_dist
with an index of positive atoms and
On Tue, Apr 2, 2013 at 12:53 PM, Elisabeth katesed...@gmail.com wrote:
Hi Justin,
Do I have to read less frames to circumvent the problem? I know g_density
has been used for this purpose so there should be a way to resolve this. I
am reading 1000 frames...
1000 frames shouldn't be a
On Tue, Apr 2, 2013 at 5:40 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
IIRC, the default Cygwin gcc is too old to compile GROMACS, as discussed on
this list in the last few months some time. I don't know how easy it is to
get a new one via the Cygwin package system.
Cygwin has the gcc
On Tue, Apr 2, 2013 at 1:09 PM, Kavyashree M hmkv...@gmail.com wrote:
Sir,
This g_hbond will generate a matrix similar to
what g_saltbr would have given in terms of variation
of distance between two charge groups.
I suppose, in that sense, the output can be useful.
I want to find out
Sir,
Thank you for the detailed insight. As you mentioned
It does not give much information. But the matrix that
it would generate would only show whether a specific
salt bridge (SB) exited at a given time within the cut-off (0.4).
I got your explanation. Yes water mediated SBs are also
Do I have to read less frames to circumvent the problem? I know g_density
has been used for this purpose so there should be a way to resolve this.
I
am reading 1000 frames...
1000 frames shouldn't be a problem, but it's an easy test to do.
Sometimes this happens with gromacs
Hi Micheal,
Just to make sure I understand you correctly -- I can have 1 type of
restraint, e.g., a harmonic potential between 2 groups defined by (k1, d1)
where k1 is force constant and d1 is the equilibrium position. But I can't
have 2 or more types of restraints like (k1,d1,k2,d2,...,kn,dn).
Hi all,
I had this problem.When i finished run the equilibration part which is
the NPT part,
and the time for this equilibration takes is about 500ps.
In here,i use the pressure 1 bar and the temperature is 300K,
But when i run the command g_energy to check the pressure of the system,
the value
On 4/2/13 7:56 PM, Nur Syafiqah Abdul Ghani wrote:
Hi all,
I had this problem.When i finished run the equilibration part which is
the NPT part,
and the time for this equilibration takes is about 500ps.
In here,i use the pressure 1 bar and the temperature is 300K,
But when i run the command
Hello,
I am calculating the hydrogen bond life time for my system.
Do program consider the hydrogen bond criteria for calculation of
autocorrelation function?
Nilesh
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the
Just calculate the radial distribution function from particle-to-particle.
You can then integrate that probability to get a mass density at a given
radius, using the average overall system density.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences,
Thank you sir for the nice suggestion
On Wed, Apr 3, 2013 at 9:58 AM, Dallas Warren dallas.war...@monash.eduwrote:
Just calculate the radial distribution function from particle-to-particle.
You can then integrate that probability to get a mass density at a given
radius, using the average
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