Dear Gromacs users!
Commonly I analyze my MD trajectories by means of covariance analysis
(projections onto some PC made by g_anaiegn).
>From that projections I've often observe several highly populated
basins corresponded to the most populated regions of the collective
space where the system spe
Sir,
Thank you for the reply. As per the suggestion, I tried increasing the
rlist. Note or warning stopped when rlist was increased to 1.8. Also with
this value of rcoulomb, the box size also needs to be increased. I would
like to know whether it is fine to keep rlist 1.8 and also whether there is
Sir,
My purpose was to compare two simulations of the
same protein at different temperatures. So I wanted
to see how the interaction of each residue with other
residues, within a cut-off, varies between the two.
by using the matrix of C-alpha contact over the whole
trajectory.
Thank you
kavya
On
Hello Sir,
I used C-alpha atoms.
Kavya
On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund wrote:
> Hi,
>
> With -r2 one can provide a second, larger, cutoff so that contact kinetics
> can be analyzed within the Luzar-Chandler framework that were designed for
> hbonds.
>
> What index groups did you
On 2/18/13 10:21 AM, Ansuman Biswas wrote:
Original Message
Subject: md with multiple ligands
From:ansuman@localhost
Date:Mon, February 18, 2013 8:28 pm
To: gmx-users@gromacs.org
-
On 2/18/13 9:54 AM, Biswajit Gorai wrote:
Dear Justin,
Thanks a lot for your reply.
As u mentioned, I edited the mass as follows:
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeBch
argeB
1 CA 1GDM C1 10.99610 12.010
Hi,
With -r2 one can provide a second, larger, cutoff so that contact
kinetics can be analyzed within the Luzar-Chandler framework that were
designed for hbonds.
What index groups did you use?
Erik
On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote:
Dear users,
As Suggested by Erik, I use
Dear users,
As Suggested by Erik, I used g_hbond with -contact to obtain a matrix of
each contact as a function of time. I used the following command -
g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e 4400 -hbn
c.ndx
I get only three contacts in the index file. The protein is a d
Original Message
Subject: md with multiple ligands
From:ansuman@localhost
Date:Mon, February 18, 2013 8:28 pm
To: gmx-users@gromacs.org
--
Message: 8
>> Da
Message: 8
>> Date: Wed, 13 Feb 2013 08:28:00 -0500
>> From: Justin Lemkul <[hidden email]>
>> Subject: Re: [gmx-users] md with multiple ligands
>> To: Discussion list for GROMACS users <[hidden email]>
>> Message-ID: <[hidden email]>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
Dear Justin,
Thanks a lot for your reply.
As u mentioned, I edited the mass as follows:
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeBch
argeB
1 CA 1GDM C1 10.99610 12.01
2 N2 1GDM N1
On 2/18/13 6:29 AM, Biswajit Gorai wrote:
Dear GMX Users,
Past few months I am struggling to unfold my protein using Guanidinium
(GDM) solutions (3,4,5,6 M).
I already did temperature (upto 498 K) induced unfolding, and able to get
expected results in 60 ns.
For GDM (6M), I did simulation upto
Thank you very much David
Cuong
On 18 February 2013 17:40, David van der Spoel wrote:
> On 2013-02-18 10:16, Cuong Nguyen wrote:
>
>> Dear Gmx-users,
>>
>> I have ions.itp file for polarized Na+ and Cl- as follows:
>>
>>
>> ; Sodium, Na+
>> [ moleculetype ]
>> ; molnamenrexcl
>> Na+
On Mon, Feb 18, 2013 at 12:10 PM, Mark Abraham wrote:
> b) a particle needs to be at that immobile reference point - you can
> measure a distance to a point whether or not there is something there.
I'm not sure that it's the same use-case... I recently talked to
someone trying to define such a fi
On Mon, Feb 18, 2013 at 5:24 AM, Wui Zhuan Lim wrote:
>
> Hi all,
>
> I'm a beginner in using Gromacs and MD simulation works.
> I am currently doing a simulation of enzyme unfolding.
> When I began NVT equilibration, a warning note appeared, as shown below:
> With twin range cut-offs and SHAKE th
On Mon, Feb 18, 2013 at 4:27 AM, ramesh cheerla wrote:
> Dear Mark,
>
> Thank you very much for your reply,
> As I am performing meta-dynamics simulations in GROMACS with PLUMED patch
> grid, I want the distance between the immobile atom and the mobile atom
> to be my collective variable. If I
Dear gmx users
I would like to smoothly decrease the strength of the interaction of coulomb &
vdw to zero, without Ewald.
According to the tutorial, I made .mdp file by myself.
MD calculation could run actually, but I am a little anxious..
Could you please tell me the following file looks corre
On 2013-02-18 10:16, Cuong Nguyen wrote:
Dear Gmx-users,
I have ions.itp file for polarized Na+ and Cl- as follows:
; Sodium, Na+
[ moleculetype ]
; molnamenrexcl
Na+1
[ atoms ]
; idat typeres nrresidu nameat namecg nrcharge
1Nac1Na+Nac1
Dear Gmx-users,
I have ions.itp file for polarized Na+ and Cl- as follows:
; Sodium, Na+
[ moleculetype ]
; molnamenrexcl
Na+1
[ atoms ]
; idat typeres nrresidu nameat namecg nrcharge
1Nac1Na+Nac11+0.312403
2Nas1Na+
19 matches
Mail list logo
