On Wed, Apr 3, 2013 at 4:56 AM, Elisabeth wrote:
> Hi Vitaly,
>
> I realize that when one extends the Z direction the resulting interface is
> liquid-vacuum, but I see that even at T below boiling point some molecules
> still leave the interface and enter the empty zone and are added to the
> oth
Thank you for responce and explanation!
So is it a good alghorithm to use gromacs genrestr command and then
include this posre.itp file into topology (without any changes) after
insertion of a ligand.itp?
Thank you in advance
On 4/2/13 6:07 AM, alex rayevsky wrote:
Dear All!
I have a doubt ab
Thank you sir for the nice suggestion
On Wed, Apr 3, 2013 at 9:58 AM, Dallas Warren wrote:
> 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.
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, M
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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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 g_e
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 is
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). Is
> >
> > 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 wit
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
interesti
On Tue, Apr 2, 2013 at 1:09 PM, Kavyashree M 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 the variatio
On Tue, Apr 2, 2013 at 5:40 AM, Mark Abraham wrote:
> 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 package which is 3.4.4
On Tue, Apr 2, 2013 at 12:53 PM, Elisabeth 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 problem, but it's an
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
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 wri
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
Thank you justin.
I will do the same.
On Tue, Apr 2, 2013 at 10:06 PM, Justin Lemkul 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 REMD
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 wrote:
>
>
> On 4/2/13 11:57 AM, Elisabeth wrote:
>
>> Dear all
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
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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 X
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 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 su
On 4/2/13 7:38 AM, Erik Marklund wrote:
On 2 Apr 2013, at 13:30, Justin Lemkul 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 searc
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 e
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 ( Other)
On Apr 2, 2013, at 5:47 PM, Albert 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 single precision.
B
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
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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 wrote:
> Dear users,
>
> Kindly clarify my doubt regarding salt bridge calculation.
>
> Thank y
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 with
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 6:4
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
> Dear friends ,
> Thank you justin and Mark for your suggestion
>
> I increases my temp range from 310-360 K
> Now I get 20 replicas
Dear friends ,
Thank you justin and Mark for your suggestion
I increases my temp range from 310-360 K
Now I get 20 replicas .
Is in such large temp range wlll it be good to use NPT.
Would you tell me the temp differences in which box instability generally
arises ..
Is my working-flow right or
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 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 mention two
>
On 2 Apr 2013, at 13:30, Justin Lemkul 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 Archive fo
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 syst
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 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 (
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 (genres
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 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 kno
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.
ht
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
st
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 script
Sorry, meant to post this on the bb.
Gesendet: Dienstag, 02. April 2013 um 11:50 Uhr
Von: "lloyd riggs"
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 atmosphere, without
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 wrote:
> On Mon, Apr 1, 2013 at 8:58 AM, 라지브간디
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 8:2
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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