jaimohan sm wrote:
Helo to all Gromax users...
I am very interesting to working in small molecules...ie calculating
energy in the sense by using thermodynamic laws.
Is there is any chance to minimise the energy for a small fragment of
proteins ..may be ligand binding site or an cavity portion.
Helo to all Gromax users... I am very interesting to working in small molecules...ie calculating energy in the sense by using thermodynamic laws. Is there is any chance to minimise the energy for a small fragment of proteins ..may be ligand binding site or an cavity portion. Without disturbing t
HI,
I have run an Md simulation of the Wild-type and the
mutant forms of a protein. I would like to analyze the
simulations for any structural changes that might have
occured upon mutation. I have carried out the usual
rmsd and rmsf analysis and observe changes. I want to
know whether there is any
Nuri A Temiz wrote:
Dear Mark
The mdp file is how it should be. I also did a cut-off run from the same
starting point and it runs.
For the PME i have tried to decrase the time step to 1 fs. that did not work
either. The protein is exploding and simulations is crashing.
OK. Take your cutoff
Maxim Fedorov wrote:
Thank you for your message, but ...
It doesn't seem to answer for my particular question -
probably I should go in more details.
I am investigating the charge-driven unfolding of protonated polypetides
like poly-L-Lysine and other compbinations of
charged/neutral residials.
Brian Stephenson wrote:
I have played around with tau_p, even increasing it to very high values
such as 100
and still get the pressure scaling problems. I've also energy minimized
many times,
to no avail. For this particular system I've been thinking there isn't
anything very
unphysical going
Hi Maxim,
On Mon, 2006-02-27 at 16:56 +, Maxim Fedorov wrote:
> Dear Daniela,
>
> > If the molecule you want to analyse is a single molecule, the
> > jumping of
> > box boundaries does not matter and the analysis tools take that into
> > account. But if your molecule is a complex of two or
Brian Stephenson wrote:
I have played around with tau_p, even increasing it to very high values
such as 100
and still get the pressure scaling problems. I've also energy minimized
many times,
to no avail. For this particular system I've been thinking there isn't
anything very
unphysical going
I have played around with tau_p, even increasing it to very high values
such as 100
and still get the pressure scaling problems. I've also energy minimized
many times,
to no avail. For this particular system I've been thinking there isn't
anything very
unphysical going on ... for some of the s
Dear Daniela, dear all.
Sorry, my previous reply was corrupted
by our server - as a result it lost any sense.
You wrote:
>
> If the molecule you want to analyse is a single molecule, the
> jumping of
> box boundaries does not matter and the analysis tools take that into
> account. But if your m
I can't help you directly, because I never tried to dock nucleic acids.
I also don't know, if autodock is generally able to recognize them.
The best thing, you can do, is writing a script, which does the renaming
of the PDB-entries in that way, autodock is able to understand them.
Regards
Maik
> --
>
> Message: 7
> Date: Mon, 27 Feb 2006 09:11:14 +0100
> From: David van der Spoel <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Counterions: influence on protein dynamics.
> To: Discussion list for GROMACS users
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type:
Dongsheng Zhang wrote:
Dear all,
Has anyone used -check14 for grompp? When I tried it just now, I got
segmentation fault. grompp works fine without the option -check14 (or
with the option -nocheck14). The error message is as follows:
grompp -f md01.mdp -c ala5 -p ala5 -check14 -o full
Back Off!
We also had those "problems".
It would be a great advancement to modify GROMACS, as David mentioned.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Dear all,
Has anyone used -check14 for grompp? When I tried it just now, I got
segmentation fault. grompp works fine without the option -check14 (or
with the option -nocheck14). The error message is as follows:
grompp -f md01.mdp -c ala5 -p ala5 -check14 -o full
Back Off! I just backed up mdout.m
Dear Daniela,
> If the molecule you want to analyse is a single molecule, the
> jumping of
> box boundaries does not matter and the analysis tools take that into
> account. But if your molecule is a complex of two or more separate
> subunits, you might want to remove jumps over the boundaries to
Dear David and Tsjerk,
Thank you very much for your answers -
I'll take care now about the PBC treatment of trajectories.
All the best,
Maxim
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please do
Dear Mark
The mdp file is how it should be. I also did a cut-off run from the same
starting point and it runs.
For the PME i have tried to decrase the time step to 1 fs. that did not work
either. The protein is exploding and simulations is crashing.
alpay
Date: Sat, 25 Feb 2006 16:57:42 +110
>but what is the meaning of " repl pr " ?
It means replica exchange probability .
>i noticed that when "X" symbol appearing , most of the value of " repl
pr" >appoarch 1.0.But in some cases, the value is about 0.2-0.3, also
the "X" >symbol appears.
>So i don\'t really catch the point about th
[EMAIL PROTECTED] wrote:
Hi,
I'm trying to EM a SDS bilayer.
It seems everything is correct, however the mdrun exits with the
following error:
Getting Loaded...
Reading file topol.tpr, VERSION 3.2.1 (single precision)
Fatal error: calloc for ilist->iatoms (nelem=-1073805064, elsize=4, file
tpx
Hi,
I'm trying to EM a SDS bilayer.
It seems everything is correct, however the mdrun exits with the
following error:
Getting Loaded...
Reading file topol.tpr, VERSION 3.2.1 (single precision)
Fatal error: calloc for ilist->iatoms (nelem=-1073805064, elsize=4, file
tpxio.c, line 712): Cannot all
Hi GMXIONS,
I am trying to perform docking of em structure of RNA from gromacs
using Autodock. Initially I converted
the gro file to pdb formated. The force field I use for GROMACS for RNA
simulation is AMBER99. Now how to convert
the pdb output of RNA from gromacs to AutoDock pdbqs. I t
Hi,Do note how the jumps are removed. First of all, this is done atom-wise. For the first frame, the position of each atom is checked against the position in the given reference, and if there's a distance between them larger than half the box vector, it is shifted back over the lattice. For each su
xu yechun wrote:
Dear all,
When I submit a optimization (double precision optimization under
vacuum condition) job to GROMACS 3.3, the error information was shown as
that listed below. However, with the same structure and parameters, the
optimization can be done well using GROMACS 3.2.1. T
Dear all,
When I submit a optimization (double precision optimization under
vacuum condition) job to GROMACS 3.3, the error information was shown as
that listed below. However, with the same structure and parameters, the
optimization can be done well using GROMACS 3.2.1. Then I submit the
[EMAIL PROTECTED] wrote:
Dear all users :
I was testing REMD swap probability with gmx3.3 a few days.
Something make me confused : if it\'s successful to exchange properties of
system between two temperatures ,
and there should be a "X" between them, like this: 2 X 3
but what is the meaning of
Dear all users :
I was testing REMD swap probability with gmx3.3 a few days.
Something make me confused : if it\'s successful to exchange properties of
system between two temperatures ,
and there should be a "X" between them, like this: 2 X 3
but what is the meaning of " repl pr " ?
i noticed t
Dear all users :
I was testing REMD swap probability with gmx3.3 a few days.
Something make me confused : if it\'s successful to exchange properties of
system between two temperatures ,
and there should be a "X" between them, like this: 2 X 3
but what is the meaning of " repl pr " ?
i noticed t
Maxim Fedorov wrote:
Dear all,
I am doing MD simulations of some polypeptide chains. These
polypeptides have non-zero net charge; therefore, I should add some
counterions into the box to use the PME.
I am wondering – is there an elegant way to reduce influence of these
counterions on polypept
Daniela S. Mueller wrote:
Dear Maxim, dear David,
On Sun, 2006-02-26 at 22:34 +0100, David van der Spoel wrote:
Maxim Fedorov wrote:
Dear all,
I have been successfully using Gromacs for a couple years without
bothering you -
manual + reading the mailing list was completely enough.
But … t
Anthony Cruz Balberdi wrote:
Hi:
I am using the g_sas with the -or option . The output file have 3 colums: first the res number, second the sasa value,
third I dont know. To what corresponds the third columnin the file?
A quick peak in the source code:
fluc2 = res_area2[res]-sqr(res_ar
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