Stéphane Téletchéa wrote:
I'm probalby doing something wrong but since neither the manual nor the
mailing list has driven me to the correct answer, i'm asking you the
problem. Thanks in advance for you answers and time.
I want to simulate my system with short NVT (for temperature
equilibratio
Michal Walczak wrote:
Dear Gromacs users,
I'd like to ask if anyone could tell me how to open *.rms file in
xmgrace, if it's possible of course or how to convert such a file into
*.xvg? That *.rms file is an output from NWChem.
Are the xmgrace or NWChem mailing lists the right places to be a
See section 5.6 of the manual, in particular 5.6.2 Basically, you have
two .itp files then you call them within the .top file using an include
command.
For solvation, doesn't matter what the topology is, solvation involves
simply adding water molecules to the coordinate file, .gro So just take
t
Hi,
I want to perform a simulation of CNT-protein interaction. I have a
topology file for the carbon nanotube alone and a topology file for the
protein alone. I don't know how to combine them, and if after them the
result can be solvated as usual using genbox. Your help is much appreciated,
Dear Gromacs users,
I'd like to ask if anyone could tell me how to open *.rms file in xmgrace,
if it's possible of course or how to convert such a file into *.xvg? That
*.rms file is an output from NWChem.
Best wishes,
Michal Walczak
___
gmx-users mai
On May 3, 2007, at 5:36 PM, Jones de Andrade wrote:
Hi Erik.
I was thinking something about it exactly now. I mean, Berk quoted
that the scalling goes with beta/tau in Berendsen, and with beta/
tay^2 in Parrinello. I mean, in a similar implementation, how
should it go for a nosè implement
I'm probalby doing something wrong but since neither the manual nor the
mailing list has driven me to the correct answer, i'm asking you the
problem. Thanks in advance for you answers and time.
I want to simulate my system with short NVT (for temperature
equilibration) and then NPT since i've
Rui Li a écrit :
Dear all,
I ran a simulation of a ligand bound to an enzyme.
When I check the pdb file,I find the residue sequence number has been modified.
But I want to preserve the original sequence number.Does anyone knows how I can
do
this ?
thanks in advance
Have a look on the mailing
Hi Erik.
I was thinking something about it exactly now. I mean, Berk quoted that the
scalling goes with beta/tau in Berendsen, and with beta/tay^2 in Parrinello.
I mean, in a similar implementation, how should it go for a nosè
implementation?
Also, what would be a good value for tau_p so? I was
On 5/3/07, Erik Lindahl <[EMAIL PROTECTED]> wrote:
Hi,
On May 3, 2007, at 12:37 PM, Jones de Andrade wrote:
Hi Berk! Thanks for your so fast answer!
I'll try to look for a different tau_p. I would really feel 4 ps a too
high value, even for water systems, but will look around before decision.
> Date: Thu, 3 May 2007 23:42:28 +1000> From: [EMAIL PROTECTED]> To:
> gmx-users@gromacs.org> Subject: Re: [gmx-users] PVT-simulation> > Jiang ran
> wrote:> > Hello everybody,> > > > Thank you all for your suggestions ,> > I
> red the Gromacs software package manual but found that PVT was not
3 maj 2007 kl. 15.42 skrev Mark Abraham:
Jiang ran wrote:
Hello everybody,
Thank you all for your suggestions ,
I red the Gromacs software package manual but found that PVT was
not
implemented yet in the Gromacs software package. I want to conserve
both volume and pressure because my p
Zuzana Benkova wrote:
I have run an NVE simulation of decamer of glycin first with PBC
(coulombtype=Cut-off) and later without PBC (coulombtype=PME).
You can't have a non-periodic system with PME.
The
gen-temp was set to 300K with option gen-vel=yes. The temperature start
to raise during sim
Jiang ran wrote:
> Hello everybody,
>
> Thank you all for your suggestions ,
> I red the Gromacs software package manual but found that PVT was not
> implemented yet in the Gromacs software package. I want to conserve
> both volume and pressure because my professor says that they are both
>
I have run an NVE simulation of decamer of glycin first with PBC
(coulombtype=Cut-off) and later without PBC (coulombtype=PME). The gen-temp
was set to 300K with option gen-vel=yes. The temperature start to raise
during simulation and finaly the following messages appeared in log file
Shake did no
test
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> Date: Thu, 26 Apr 2007 15:52:10 +0200> From: [EMAIL PROTECTED]> To:
> gmx-users@gromacs.org> Subject: Re: [gmx-users] PVT-simulation> > Jiang ran
> wrote:> > Hello everybody,> > My name is called Jiong and I'm new to the
> GROMACS simulation software > > package and the field of MD.> > I have
Thanks very much for you advises.
Actually I just made one molecule of dppc using
information from leterature about its bond lenghts and
angles and so on... and then run md with that one
molecule and then multipled it. First I made 16 dppc
bilayer with 480 water and then from that 16dppc I
made 32
Hi,
On May 3, 2007, at 12:37 PM, Jones de Andrade wrote:
Hi Berk! Thanks for your so fast answer!
I'll try to look for a different tau_p. I would really feel 4 ps a
too high value, even for water systems, but will look around before
decision. Anyway, I'm still concerned about the compressi
Hi Berk! Thanks for your so fast answer!
I'll try to look for a different tau_p. I would really feel 4 ps a too high
value, even for water systems, but will look around before decision. Anyway,
I'm still concerned about the compressibility value.
Long time ago in this list I came to this questio
From: "Jones de Andrade" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "Discussion list for GROMACS users"
Subject: [gmx-users] Compressibility issue - real concern
Date: Thu, 3 May 2007 06:33:12 -0300
Hi all.
Well, I'm having a great problem in some NpT simulations I
Hi all.
Well, I'm having a great problem in some NpT simulations I'm running here,
which leaded me to some concerns. Let me try to explain the situation:
Ok, I know: everywhere, including this list, amber list and any
computational chemistry list informs that the compressibility of the liquid
do
Hi,
I would say that in most cases when you only want to remove rotation
in the xy plane, you also only want to remove translation in the xy plane.
But apparently for your system this is not the case.
I have just fixed a bug in the xy fit that could cause mirror imaging
of the system (I indeed h
Mark Abraham wrote:
Tsjerk Wassenaar wrote:
Hi Andrea,
On 5/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
Andrea Robben Browning wrote:
> I am trying to cut out a portion of a large equilbrated crystal to
make
> a smaller crystal. I have been using the genbox command but since it
> tries to
hi,
On Thursday, 3. May 2007 09:03, Mark Abraham wrote:
> David van der Spoel wrote:
> > The one single reason for combining these things would be the abilitiy
> > to reuse Joomla passwords. We already have separate passwords for
> > bugzilla, website and mailing lists. On the other hand since br
David van der Spoel wrote:
The one single reason for combining these things would be the abilitiy
to reuse Joomla passwords. We already have separate passwords for
bugzilla, website and mailing lists. On the other hand since browsers
memorize passwords for you it may not be that big a deal.
W
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