Thanks for your answer.
Actually no my run did not finish normally the first time (it has been
stopped after 7 days because of the time limitation on the cluster it was
running on). So I started it again (I ran the same command and added the
option "-append yes") and this time the calculation
Hi
Thanks a lot for help. I could run the EM with ATP in its right place. But
position restrained dynamics gives warnings saying that some angles are rotated
beyond 30 deg. So when i directly went for MD run it is running fine. What
dis-advantages i have of not performing position restrained dy
We are running SUSE Linux
It's best to keep all of this on the mailing list in case it becomes
useful to somebody else.
jayant james wrote:
Hi!
thanks for your mail. I have never used pull code before and so I am a
bit apprehensive but I do accept your suggestion and I am working on
that.
Let me re-emphasize that the pull code may be a good solution for you.
As per your request, I currently use the following without any problems:
fftw 3.1.2
gromacs 3.3.1 or 4.0.4
openmpi 1.2.6
Be especially aware that openmpi 1.3.0 and 1.3.1 are broken, as I posted
here:
http://lists.gromacs.
Why not use the pull code? If you haev to use distance restraints,
then try LAM mpi with your pd run. We had similar error messages with
vanilla .mdp files using openmpi with large and complex systems that
went away when we switched to LAM MPI. Our problems disappeared in gmx
4 so we went b
Dear gmxusers
I want to calculate the angle between 2 alpha helix. One of the
possibility to do, is g_bundle command. If I want to use g_bundle I have a
problem to define the groups in the index file. On a basis of which
criteria could I choose the 3 group in index file as input for g_bundle???
B
The energy minimization went on without any problem on 4 processors but the
problem occurs when I perform the MD run. Also, I did not get any error
message with relevance to LINCS etc...
JJ
On Wed, Jun 24, 2009 at 6:53 PM, Justin A. Lemkul wrote:
>
>
> jayant james wrote:
>
>> Yes my distance re
Alexandre Suman de Araujo wrote:
Hi Mark
Do you know any site/paper/book which clearly discuss the use of other
network paradigms (infiniband, myrinet, etc) to perform fair parallel MD
simulations?
No. GROMACS will work over any network across which you can run MPI. For
MD, you are likely t
Hi Mark
Do you know any site/paper/book which clearly discuss the use of other
network paradigms (infiniband, myrinet, etc) to perform fair parallel MD
simulations?
Thanks!
**
Alexandre Suman de Araujo
Morteza Khabiri wrote:
Dear gmxusers
I want to calculate the angle between 2 alpha helix. One of the
possibility to do, is g_bundle command. If I want to use g_bundle I have a
problem to define the groups in the index file. On a basis of which
criteria could I choose the 3 group in index file as
Dear gmxusers
I want to calculate the angle between 2 alpha helix. One of the
possibility to do, is g_bundle command. If I want to use g_bundle I have a
problem to define the groups in the index file. On a basis of which
criteria could I choose the 3 group in index file as input for g_bundle???
B
I do not see topology file in your archive.
2009/6/25
> The input files for EM of the job are in the attachment.
>
>
>
> Thank you for your time!
>
>
> - 原始邮件 -
> 发件人：Vitaly V. Chaban
> 收件人：toby10222...@sina.com, gmx-users@gromacs.org
> 主题：Re: 回复：Re: 回复：[gmx-users] Re: How to freeze th
akalabya bissoyi wrote:
Thanks gromacs
for you replay, can any body provide tutorial/standard protocol how to
use of LAN for parallel processing.
The canonical guide for doing installations of MPI versions of GROMACS
can be found here http://oldwww.gromacs.org/content/view/19/32/
Mark
___
Hi,
As I said, if you set a reference group (any name/group for pull_group0),
you apply a potential between two groups group0 and group1.
These two groups are treated completely equivalently (they both
experience the same force, but with opposite sign and they will both move
under influence of th
Thanks gromacs
for you replay, can any body provide tutorial/standard protocol how to use
of LAN for parallel processing.
AKALABYA BISSOYI
N.I.T.Rourkela
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo
Bernhard Knapp skrev:
The whole complex consists of 5 chains (MHC-alpha, MHC-beta, epitope,
T-cell receptor alpa, T-cell receptor beta).
What you can see in
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg
is exactly
What is meant by absolute reference? Can it be the Origin (0, 0, 0).
Does it assume a random reference point for the pullx.xvg? I get a
negative value for my first pulling group, even though it is inside
the box and above the origin. Furthermore 0-Zcoord(pullgrp) doesn't
fit either.
Does it
The whole complex consists of 5 chains (MHC-alpha, MHC-beta, epitope,
T-cell receptor alpa, T-cell receptor beta).
What you can see in
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg
is exactly the same angle. The two
Bing Bing wrote:
Hi! Thanks a alot for all the suggestions i've got from Justin and Mark.
I found out that i actually deleted the box information from the
starting structure PDB. Once i put it back, It worked. However,
it stopped with this message.
Stepsize too small, or no change in energy.
C
Hi! Thanks a alot for all the suggestions i've got from Justin and Mark.
I found out that i actually deleted the box information from the starting
structure PDB. Once i put it back, It worked. However,
it stopped with this message.
Stepsize too small, or no change in energy.
Converged to machine p
> Date: Thu, 25 Jun 2009 18:39:53 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: Re: problems with some calculated trajectories
>
> Bernhard Knapp wrote:
> > 1) trjconv with the "-pbc nojump" option does not help - it removes most
>
> If I und
Bernhard Knapp wrote:
1) trjconv with the "-pbc nojump" option does not help - it removes most
If I understand correctly, -pbc nojump will help when the relevant atoms
are part of the same [moleculetype]. One fragment in each of your two
examples is apparently the same four-strand sheet with
Hi Bernhard,
The images, are they taken from exactly the same angle? If so, there's
some change in orientation that is just impossible in such a short
time. You didn't happen to fit your structure to a reference prior to
removal of jumps, did you? Fitting messes up PBC and garbles results
from -pb
1) trjconv with the "-pbc nojump" option does not help - it removes most
of the jumps but one big remains- the rmsd for the trajectory is
http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg
before the converting with -pbc and
http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg
after conversion.
in
Hi Subarna,
If you just want to retain the structure of the cluster it doesn't
matter too much. It may be good to average values from different
structures, though. HOWEVER, an FeS cluster is a catalytic site, which
probably has fancy electronic properties, which may well affect the
behaviour of th
Hi,
I don't think that is a good idea.
I put the following advise in grompp
"Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge groups
can lead to serious cut-off artifacts.\n"
"For efficien
Dear gmx users,
Can N(CH2)3 be set a charge group? Is it too large to set? Any reply would be
thanked very much.
Sincerely
Chaofu Wu
_
打工，挣钱，买房子，快来MClub一起”金屋藏娇”！
http://club.msn.cn/?from=10___
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