Dear Gromacs users
-- Iam trying to perform free energy calculation for
protein-ligand complex.
--Can any one plz suggess an appropriate tutorial to be
follow to perform this analysis
--
Thanks & Regards
N.NagaSundaram
--
gmx-users mailing listgmx-users@gromacs.org
http
Hi
Plz try -pbc nojump option...It may work
On Wed, Feb 13, 2013 at 5:29 AM, 라지브간디 wrote:
> Dear gmx users,
>
>
> I need to stop my protein jumping inside box. I have used -pbc mol -ur
> compact -center command too but still the protein gets moving from one
> place to other.
>
>
> Could
Dear users
I performed 20 ns simulation for protein complex. After 10
ns only my system obtained equilibration state .
I would like to analyze last 10 ns from the trajectory
file.I got problem to generate last 10 ns xtc file from the 20 ns trr file.
Thanks justin got it...
On Wed, Oct 3, 2012 at 4:10 AM, Justin Lemkul wrote:
>
>
> On 10/3/12 6:10 AM, naga sundar wrote:
>
>> Dear friends
>>
>>Unfortunately my MD run got stopped. While i tried to
>> append
>> the run with command li
Dear friends
Unfortunately my MD run got stopped. While i tried to append
the run with command line
mdrun -s fws_md.tpr -cp state.cpt -append, its not get
appending, its again get restart.
What should be the problem.I need to append my run.
--
R
Dear Pramod
use the command
xmgrace -nxy file1.xvg file2.xvg
Instead of file1 and file2 use ur file name.
On Tue, Oct 2, 2012 at 8:49 PM, ram bio wrote:
> Dear Gromacs users,
>
> I am trying to find inter atomic distances between ligand ato
n abnormally high
> value by subtracting half the x/y dimension of the box from its coordinates
> and re-calculate the rmsd , but I think trjconv would do it as well.
>
> Felipe
>
>
> On 09/25/2012 09:22 AM, naga sundar wrote:
>
>> Dear justin
>>
>
looking at is not centred properly. If it isnt you just have to centre
> it.
> > >
> > > Stephan
> > >
> > > Original-Nachricht
> > >> Datum: Mon, 24 Sep 2012 04:32:33 -0700
> > >> Von: naga sundar
&
/S0006291X08020792.
Overall, all the factors are supporting our results. So shall we take this
RMSD analysis as good result . Even after repeating the 20 ns MD simulation
two times i got the same results.
On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul wrote:
>
>
> On 9/24/12 6:24 AM, na
Dear gromacs users
We performed MD simulation analysis for native and mutant
models of protein-protein complexes. From 20 ns simulation trajectory, we
generated RMSD graph for one native and three mutant complexes. For native
complex in the entire simulation period, we observed a cons
Dear simone
I think so u r using the same pr.mdp and md.mdp files
what u created initially. So open both the mdp files replace DRG with UNK
and the try sure it will work out.
On Tue, Sep 18, 2012 at 9:44 AM, Justin Lemkul wrote:
>
>
> On 9/18/12 12:42 PM, SIMONE BROGI wrote:
Dear gromacs users
I run 20 ns MD simulation for protein mutant complexes. In RMSD analysis
at ~9 ns sudden increase in the deviation was observed from 0.2 nm to 1.7
nm and immediate fall was observed.
I rerun the 20 ns simulation for the same molecule with same procedure.
While analyzing the RM
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