-- Forwarded message --
From: 秦姗姗 <[EMAIL PROTECTED]>
Date: Aug 30, 2007 3:12 AM
Subject: thanks very much, I know where I am wrong
To: Tsjerk Wassenaar <[EMAIL PROTECTED]>
Dear Wassenaar:
I know why my NPT simulation always crash: I made a very
stupid mistake, I used
I'm doing MD Simulation on self-assembly of lipid molecules using
gromacs. If someone can kindly help me find the conditions (for my
.mdp file) for these kind of simulation? There are many choices and
i would like to ask for opinion on general (usually) conditions used
in the .mdp fil
Hi Li,
I think g_cluster will do a removing of translation and rotation
displacement automatically. I am not quite sure whether it will do such
part on the group of atoms I pick in the index file? If so is there any
way I can specify which region to do the removement or if I can simply
turn o
Hi,
The GROMACS user manual is a good place to start. For more specific help you
will probably need to provide details of exactly what you want to do.
What are you simulating? What are the questions you are hoping to answer?
Best wishes,
-Syma
**
Dear Gromacs users,
I'm doing MD Simulation on self-assembly of lipid molecules using gromacs. If
someone can kindly help me find the conditions (for my .mdp file) for these
kind of simulation? There are many choices and i would like to ask for opinion
on general (usually) conditions used
Marcus Kubitzki writes:
Hi Li,
first, generate an appropriate index file with make_ndx. There you can
select the loops you want to analyze. Second, run g_cluster -s -f -n.
Marcus
Li Su wrote:
Dear Sir/Madam,
I am trying to use g_cluster to clusterize my protein trajectories. The
proein co
[EMAIL PROTECTED] wrote:
Hi David
Thank you very much for the reply! So, which group, in the end, shall I select
in g_dipoles to see the dipole? And how to use trjconv after editconf the way
you told me? (the input/output of editconf is a .gro file and of trjconv is
.trr/.xtc files) And whose
Hi David
Thank you very much for the reply! So, which group, in the end, shall I select
in g_dipoles to see the dipole? And how to use trjconv after editconf the way
you told me? (the input/output of editconf is a .gro file and of trjconv is
.trr/.xtc files) And whose group shall I select in th
You can check out the Gromacs Wiki pages:
http://wiki.gromacs.org/index.php/Development
http://wiki.gromacs.org/index.php/CVS_HowTo
Bob
On 8/29/07, Arturas Ziemys <[EMAIL PROTECTED]> wrote:
>
> How to access CVS of GROMACS ?
>
> Robert Johnson wrote:
> > The CVS version of Gromacs enables REMD si
How to access CVS of GROMACS ?
Robert Johnson wrote:
The CVS version of Gromacs enables REMD simulations where each replica
can be run across multiple CPUs.
Bob
On 8/29/07, Arturas Ziemys <[EMAIL PROTECTED]> wrote:
Hi,
After I was reading manual on REMD and mdrun, I understood that GROMACX
i
The CVS version of Gromacs enables REMD simulations where each replica
can be run across multiple CPUs.
Bob
On 8/29/07, Arturas Ziemys <[EMAIL PROTECTED]> wrote:
> Hi,
>
> After I was reading manual on REMD and mdrun, I understood that GROMACX
> is capable to run REMD using just one node per repli
Hi,
After I was reading manual on REMD and mdrun, I understood that GROMACX
is capable to run REMD using just one node per replica (or single CPU
??). Is it right ?
Best
Arturas
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.
Hi Li,
first, generate an appropriate index file with make_ndx. There you can
select the loops you want to analyze. Second, run g_cluster -s -f -n.
Marcus
Li Su wrote:
Dear Sir/Madam,
I am trying to use g_cluster to clusterize my protein trajectories. The
proein core is very rigid, only loops
Dear Sir/Madam,
I am trying to use g_cluster to clusterize my protein trajectories. The
proein core is very rigid, only loops will fluctuate. When I clusterize I
want to clusterize only on the loops in stead of the whole protein. But when
I use g_cluster it only offer choices on whole protein o
Dear Shanshan Qin,
Please keep the discussions on the list. That way, you can benefit
from the input from others as well and the discussion will be
archived. Note I didn't forward your structures/topologies, since I
don't know whether it's okay that that information is archived too...
Best,
Tsje
Hi Pascal,
I found this entry in the mailing list archives:
http://www.gromacs.org/pipermail/gmx-users/2006-August/023554.html
Not only is it good practice to browse the archives when asking a
question, but it also helps to keep track of question you asked and
the answers you got. Or am I missin
From: [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users
To: gmx-users@gromacs.org
Subject: [gmx-users] RF excl and protein/water potential energies
Date: Wed, 29 Aug 2007 11:09:10 +0200 (MEST)
Dear community,
I am trying to separate potential energy contributions coming from the
Dear community,
I am trying to separate potential energy contributions coming from the protein
and from water in my solvated protein system.
Dose anybody know if the term "RF excl" can be computed / written separately
for protein / water atoms? I would be interested in the "RF excl" contributions
Hi Q733,
The large pressure fluctuation is not the cause of your problem. In
fact, the pressure will show large fluctuations in MD anyway and this
has been discussed on the mailing list numerous times and can be found
on the Gromacs Wiki. That your simulation crashes is caused by
something else, w
Hi!
I use "editconf -mead" to generate pqr files for APBS calculations. I was
checking the atomic radii and charges I obtain. The charges correspond to those
listed in my topology file, but I cannot find from which force field file the
atomic radii of the pqr were read, or how they were computed,
Dear gmx-users:
I made a lipid bilayer fully hydrated by water,without water in the
lipid hydrophobic tails.Then I minimized the energy to Fmax=132.5,then I
ran NVT md for 200ps.However when
I wanted to run NPT simulation, the pressure fluctuation was as high as
1.33*10E+05,it crashed very easily
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