Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this?
Will the removal of the periodic boundary condition be OK?
--
Sun Li
Department of Physics
Nanjing University, China
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Hi There,
I am running a long MDS for one protein molecule in water, To avoid error I
am running the simulation in parts like 20 nsec each.
Each time I am creating a new tpr, trr and edr using the tpbconv and mdrun.
Last time when I fired a job for 60-80 nsec then the job crashed because of
some po
Hi.
I'm very new to iMAC as I've just started to use it for about one month. I
would like to install GROMACS on it but i seem can't find any step-to-step
installation instruction. All those that I found was seem to be instruction
for linux. Can you give me some idea on how to get the installation
i
So,
First the bad news: from now on we're probably not going to care too
much about bugs in gromacs-3.3.
The good news is that Gromacs 4.0 is finally & officially _released_.
You can download the source code package at
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.0.tar.gz
We will put docum
Hi,
Not 4.0, but it's in the pipeline for 4.1.
The issue is not doing it, but doing it clearly faster than explicit
water MD, since water interactions are extremely optimized in Gromacs!
Cheers,
Erik
On Oct 9, 2008, at 2:38 PM, Arthur Roberts wrote:
Hi, all,
I know this question might s
Hi all,
Recently, I post one question about g_rdf under Version 3.3.3. After discussing
with Florian Dommert, and rereading the code of gmx_rdf.c, I have the following
results:
1. -nocom -rdf atom is reliable;
2. -com calculates the com of the WHOLE first group!, not the com of the
molecules/re
Dear gmx-users,
Some time ago I did a web search and I found a tutorial that showed
step by step how to compile the Gaussian 03 with interface to Gromacs
for QMMM calculations. There, the tutorial indicated the lines of the
code that should be changed and other tips. But now I can't find this
link
Hi, all,
I know this question might seem almost heretical because I am aware of
the issues with implicit water md. I actually prefer explicit waters
because I think it more realistically represents the water
environment. However, the problem with explicit waters is that the
calculation
Dear Xavier,
I am sorry for posting an email which is not directly related to the
gromacs.
I have created a trajectory which contains the time dependent orientational
changes of my reference structure (from the original trajectory generated by
gromacs). I obtained the average rotational correalti
I am using 'g_cluster' (-method gromos, version 3.3.1) to cluster the
conformations of a subset of residues in my protein from a MD trajectory and
have a couple of questions:
1. I have pre-fitted my trajectory on the 'core' of the protein and
therefore don't want g_cluster to refit my subset of re
See AFM pulling description in manual.
AFM means "Atomic force microscopy".
That`s what you neeed).
-Original Message-
From: "huifang liu" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Thu, 9 Oct 2008 14:09:05 +0800
Subject: [gmx-users] how to use gromacs for steered molecular dynam
Hi,
If you have any interested students/postdocs/other it would be great
if you could help us spread this announcement!
(There's also an online version at http://www.dbb.su.se/Vacancies )
As part of a 5-year European Union FP7 project to push GROMACS to use
next-generation hardware we are
Hi,
Great. I'll just revert to make static libraries the default for 4.0
too.
Cheers,
Erik
On Oct 9, 2008, at 7:55 AM, Justin A. Lemkul wrote:
Erik Lindahl wrote:
On Oct 9, 2008, at 5:24 AM, Justin A. Lemkul wrote:
To follow up just a bit more - it appears that this problem is
isol
Erik Lindahl wrote:
On Oct 9, 2008, at 5:24 AM, Justin A. Lemkul wrote:
To follow up just a bit more - it appears that this problem is
isolated to the PowerPC architecture. I can compile and install RC4
on my own laptop (a recent Intel Mac) with no problems.
I think it's the shared lib
shahrbanoo karbalaee wrote:
thank you justin .
would you please tell me how can it equilbrated?is it the table rmsd
aor visualization?or the time pr-md for 10 ns is enough (for tfe and
spce)?
Such information is usually based on experimental observables (density, heat
capacity, etc.) I
On Thu, Oct 09, 2008 at 02:06:30PM +, Rebeca García Fandiño wrote:
>
> Hello,
> I am trying to calculate the area per lipid for a quite big membrane formed
> by a unique type o lipid (DOPC). I can see ondulations in the membrane, so I
> am not sure of the right area I should have to employ,
thank you justin .
would you please tell me how can it equilbrated?is it the table rmsd
aor visualization?or the time pr-md for 10 ns is enough (for tfe and
spce)?
--
sh-karbalaee
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Hello,
I am trying to calculate the area per lipid for a quite big membrane formed by
a unique type o lipid (DOPC). I can see ondulations in the membrane, so I am
not sure of the right area I should have to employ, because the max and min
values in x and y axes are not representative for the re
excuse me for bad typing in english.
how can I understand the solvents file equilbrated?from rmsd or
visualization or ..?
--
sh-karbalaee
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search
On Oct 9, 2008, at 5:24 AM, Justin A. Lemkul wrote:
To follow up just a bit more - it appears that this problem is
isolated to the PowerPC architecture. I can compile and install RC4
on my own laptop (a recent Intel Mac) with no problems.
I think it's the shared libraries in combination
Hi Justin,
This might be due to shared libraries, which I thought always worked
on OS X :-)
Could you try with the option --disable-shared?
I guess the world still might not be ready for default shared
libraries... in that case I'll disable it.
Cheers,
Erik
On Oct 9, 2008, at 4:36 AM,
> Date: Thu, 9 Oct 2008 08:44:15 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] steady
>
>
>
> shahrbanoo karbalaee wrote:
> > Dear justin
> >
> > a) if I want to have the steady and hemogen for mix solvent , do I
> > have to use this command (whe
shahrbanoo karbalaee wrote:
Dear justin
a) if I want to have the steady and hemogen for mix solvent , do I
have to use this command (when I made genbox box 16.16.24 before
that)?
:editconf -f conf.gro -bt dodecahedron -d 0.5 -o box.gro
This will not homogenize anything; it only sets up
Justin A. Lemkul wrote:
David van der Spoel wrote:
Justin A. Lemkul wrote:
To follow up just a bit more - it appears that this problem is
isolated to the PowerPC architecture. I can compile and install RC4
on my own laptop (a recent Intel Mac) with no problems.
Not sure that I can help, b
Dear justin
a) if I want to have the steady and hemogen for mix solvent , do I
have to use this command (when I made genbox box 16.16.24 before
that)?
:editconf -f conf.gro -bt dodecahedron -d 0.5 -o box.gro
b) I use trjconv -pbc mol -ur compact and then minimize .when I see
the output this
David van der Spoel wrote:
Justin A. Lemkul wrote:
To follow up just a bit more - it appears that this problem is
isolated to the PowerPC architecture. I can compile and install RC4
on my own laptop (a recent Intel Mac) with no problems.
Not sure that I can help, but Erik recently fixed a
Justin A. Lemkul wrote:
To follow up just a bit more - it appears that this problem is isolated
to the PowerPC architecture. I can compile and install RC4 on my own
laptop (a recent Intel Mac) with no problems.
Not sure that I can help, but Erik recently fixed a bug report related
to CPU det
To follow up just a bit more - it appears that this problem is isolated to the
PowerPC architecture. I can compile and install RC4 on my own laptop (a recent
Intel Mac) with no problems.
-Justin
Justin A. Lemkul wrote:
A follow-up to my previous message: I've just compiled RC2 and RC3 to
A follow-up to my previous message: I've just compiled RC2 and RC3 to confirm
that nothing has changed within our system configuration; both RC2 and RC3
compile and install with no problems using the procedure in my previous message.
I am still faced with the fact that RC4 will not compile.
Hi,
It was a problem with my cluster, in particular with mvapich2 settings!
Now it works fine with rc2 and rc3!
Sorry,
Carlo
On 9 Oct 2008, at 09:35, [EMAIL PROTECTED] wrote:
Message: 4
Date: Thu, 9 Oct 2008 09:07:58 +0200
From: Berk Hess <[EMAIL PROTECTED]>
Subject: RE: [gmx-users] gromacs 4-
Hi,
Fully agree with that one. But the big problem is with simulations for
comparison that you have to justify that a bug fix could not be the
cause of a difference between simulations (or could even counteract on
something which should give a difference). So even with minor
revisions, unless you
Hi,
I agree with Tsjerk, but his mail might have not answered your question exaclty.
In general one should not switch between major revisions in one project.
But there should be nearly no differences in simulation results between
minor revisions. If there are differences this means that a bug was
Am Thursday, 9. October 2008 schrieb huifang liu:
> i want to use gromacs to pull a small ligand through a protein channel and
> study the interaction between the ligand and the protein during this
> process. However, i have not found out any useful information about steered
> molecular dynamics(S
Minnale,
Hmm, I thought I recalled answering a similar question just recently.
But mind you that doing statistics on MD, unless the results are very
obvious, you have to be as careful and consistent as can be. That
means that you should avoid trying to compare things which are
performed under diff
Hi Maria,
The answer is in the source code of course. But here's a python/pymol
function which does the same thing, and which I wrote after the
routine in editconf. It takes as input the definition as a list with
lengths x,y,z and angles a,b,c and returns the upper triangular
matrix:
def triclini
Hi,
With RC4 this works fine for me (both command lines).
Nothing seems to have changed to the filename part of the code since RC2.
Are you sure the mdrun_mpi in your path is the Gromacs 4 rc 2 binary?
(try mdrun_mpi -h)
Berk
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Date: Wed, 8
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