Hi,
FWIW, I have recently asked about this in the hwloc mailing list:
http://www.open-mpi.org/community/lists/hwloc-users/2010/10/0232.php
In general, hwloc is a useful tool for these things.
http://www.open-mpi.org/projects/hwloc/
Best,
Ondrej
On Thu, Oct 21, 2010 at 12:03, Carsten Kutzner
Hi,
thanks for fixing this, Berk. Silly me, I did not include RESOLVED
bugs in my original search and therefore missed it.
Ondrej
On Thu, Oct 7, 2010 at 12:38, Berk Hess wrote:
> Hi,
>
> It's bugzilla 579:
> http://bugzilla.gromacs.org/show_bug.cgi?id=579
> Actually the title is wrong, the pre
On Wed, Sep 29, 2010 at 21:56, David van der Spoel wrote:
>
> After setting nstcalcenergy = 1 I get
> Density 996.894 1.2 3.85083 1.86718 (kg/m^3)
>
> In other words the bug can be circumvented by setting this variable to 1. I
> will file a bugzilla.
>
Is this bug in now? I c
On Wed, Sep 29, 2010 at 21:56, David van der Spoel wrote:
>
>
> Now the differences in the tpr files are revealing:
> [anfinsen:test-volume-drift] % gmxcheck -s1 topol405.tpr -s2 topol.tpr
>
> Note: tpx file_version 58, software version 73
> Reading file topol.tpr, VERSION 4.5.1-%ci-21e8a32 (sing
the drift in box volume when run in 4.5.1. Of course, it will not
run in 4.0.7, so there is no way of testing that.
Thanks for any help on this,
Ondrej
On Thu, Sep 23, 2010 at 15:16, Ondrej Marsalek
wrote:
> Dear all,
>
> running a box of neat water with the below mdp file in GROM
Dear all,
running a box of neat water with the below mdp file in GROMACS 4.5.1
results in a fast linear increase of the volume of the box, the water
getting torn into clusters. The same simulation in 4.0.7 (with
nstcalcenergy removed, of course) runs just fine, with the box volume
stable and fluct
= 0.8
rcoulomb = 1
rvdw-switch = 0.8
rvdw = 1
On Thu, Sep 23, 2010 at 15:16, Ondrej Marsalek
wrote:
> Dear all,
>
> running a box of neat water with the below mdp file in GROMACS 4.5.1
> results in a fast linear increase of t
Hi,
thanks for the fix.
Best,
Ondrej
On Wed, Aug 11, 2010 at 08:46, Rossen Apostolov
wrote:
> Hi,
>
> I commited a patch in the latest git.
>
> Thanks for reporting,
> Rossen
>
> On 8/10/10 4:13 PM, Ondrej Marsalek wrote:
>>
>> Dear all,
>>
>&g
Dear all,
I have installed 4.5 beta2 using cmake and it seems that the GMXRC
files are missing in the installation. Can anyone confirm this?
Best,
Ondrej
--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www
Ah, now I see what you meant. Then it is fine. That is a separate
issue and is not really a problem for me.
Thank you,
Ondrej
On Tue, Nov 24, 2009 at 17:39, Berk Hess wrote:
> Hi,
>
> Sure g_rdf takes care of pressure coupling, but the cut-off of the rdf plot
> is set from the initial frame.
>
Hi again,
I thought pressure coupling is handled by g_rdf. Looking at the code,
it seems that the block starting with:
/* Must init pbc every step because of pressure coupling */
takes care of that, so even with a relatively big volume change at the
beginning, it should not be a problem. Is
On Tue, Nov 24, 2009 at 11:12, Berk Hess wrote:
> Hi,
>
> If you have N molecules with total volume which is significantly less than
> the unit-cell,
> as is the case for ions in solvent, the RDF of the N molecules againt
> themselves
> will converge to (N-1)/N.
>
> Berk
Hi,
thanks for the remin
On Tue, Nov 24, 2009 at 13:01, Omer Markovitch wrote:
>
> On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek
> wrote:
>>
>> Dear all,
>>
>> I would like to understand better the way g_rdf performs
>> normalization. I have two unexpected results:
>>
&
Dear all,
I would like to understand better the way g_rdf performs
normalization. I have two unexpected results:
1) In a simple simulation of atomic ions in water in a cubic box, I
get RDFs that clearly reach a constant value at large enough
distances, but that value is somewhat lower than one. T
s "protein" and counterions.
Any help or pointers appreciated,
Ondrej
On Mon, Nov 16, 2009 at 19:58, Ondrej Marsalek
wrote:
> I have just found that the problem (at least with trjconv) only
> manifests if I include in the options "-pbc mol". I use a dodecahedron
>
on, Nov 16, 2009 at 19:54, Tsjerk Wassenaar wrote:
> Hi Ondrej,
>
> Please paste the exact series of commands you used. That will make it
> easier to indicate where errors are being introduced.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Nov 16, 2009 at 6:53 PM, Ondrej Marsalek
&
> coordinate file from the .tpr matching the atoms in the .xtc file.
>
> Hope it helps,
>
> Tsjerk
>
> On Mon, Nov 16, 2009 at 6:22 PM, Ondrej Marsalek
> wrote:
>> Dear all,
>>
>> as a quick check, before I dive deeper, I would like to ask the following.
&
segfault
Does anyone else see this, or am I doing something wrong? Will be
happy to post more details if needed.
Ondrej
On Mon, Nov 16, 2009 at 18:22, Ondrej Marsalek
wrote:
> Dear all,
>
> as a quick check, before I dive deeper, I would like to ask the following.
>
> I ha
Dear all,
as a quick check, before I dive deeper, I would like to ask the following.
I have a simulation (protein in water and counterions) for which I
have defined an xtc output group (protein and conunterions). If I try
to run trjconv or g_dist over this xtc file (and a proper reduced
index fil
Hi,
just for reference, I have filed a bug report on this (and one other
issue with g_sdf):
http://bugzilla.gromacs.org/show_bug.cgi?id=356
Best,
Ondrej
On Tue, Nov 10, 2009 at 16:35, Rasmus "Termo" Lundsgaard
wrote:
> Hi Atte
>
> Did you find a solution to this problem?? I'm doing the same c
Dear all,
I have noticed that the .ddb file are not present in the port of the
Amber FF available at http://chemistry.csulb.edu/ffamber/. Does anyone
know if they are perhaps available elsewhere or if something has been
done in this direction?
Thanks for any information,
Ondrej Marsalek
--
gmx
On Wed, Nov 4, 2009 at 20:41, Justin A. Lemkul wrote:
>
>
> Ondrej Marsalek wrote:
>>
>> I thought that this was needed to convert the hydrogens to virtual
>> sites, based on reading section 6.5 of the manual and some other
>> things. Is this not correct?
&g
On Wed, Nov 4, 2009 at 20:41, Justin A. Lemkul wrote:
>
>
> Ondrej Marsalek wrote:
>>
>> I thought that this was needed to convert the hydrogens to virtual
>> sites, based on reading section 6.5 of the manual and some other
>> things. Is this not correct?
&g
I thought that this was needed to convert the hydrogens to virtual
sites, based on reading section 6.5 of the manual and some other
things. Is this not correct?
Ondrej
On Wed, Nov 4, 2009 at 20:07, Justin A. Lemkul wrote:
>
>
> Ondrej Marsalek wrote:
>>
>> Dear GROMACS
Dear GROMACS users,
I would like to substitute hydrogens in a protein with virtual sites
to allow for the 4-5 fs timestep mentioned in the GROMACS 4 paper and
several other places. So far, I have not found an example or a
tutorial that would involve this, so I want to create a
straightforward exam
fine even in parallel.
This looks like a bug to me, has anyone else seen this?
Best regards,
Ondrej Marsalek
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