on the login node or on the compute node?
>
I did the test on the debug queue, so it was a compute node.
Let me know if you need more info.
Best,
Dimitar
>
> Thanks
> Roland
>
>
> On Wed, Jun 8, 2011 at 1:17 PM, Dimitar Pachov wrote:
>
>> Hello,
>>
>>
was
the same as reported earlier. You could do the test there as well, if you
have access, and see what you would get.
Hope that helps a bit.
Thanks,
Dimitar
>
> Sander
>
>
>
>
>
> On Jun 7, 2011, at 23:21 , Dimitar Pachov wrote:
>
> Hello,
>
> Just a q
Hello,
Just a quick update after a few shorts tests we (my colleague and I) quickly
did. First, using
"*You can emulate this yourself by calling "sleep 10s" before mdrun and see
if that's long enough to solve the latency issue in your case.*"
doesn't work for a few reasons, mainly because it doe
On Sun, Jun 5, 2011 at 2:14 AM, Mark Abraham wrote:
> On 5/06/2011 12:31 PM, Dimitar Pachov wrote:
>
> As I said, the queue is like this: you submit the job, it finds an empty
> node, it goes there, however seconds later another user with
> higher privileges on that particular nod
On Sat, Jun 4, 2011 at 9:09 PM, Mark Abraham wrote:
> On 5/06/2011 3:11 AM, Dimitar Pachov wrote:
>
On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham
> wrote:
>
> On 4/06/2011 8:26 AM, Dimitar Pachov wrote
>>
>>
> Here is an example:
>
> ===
On Sat, Jun 4, 2011 at 1:50 PM, Rossen Apostolov wrote:
> Hi,
>
> On Jun 4, 2011, at 19:11, Dimitar Pachov wrote:
>
> By the way, is this ever reviewed:
>
> "Your mail to 'gmx-users' with the subject
>
>Re: [gmx-users] Why does the -append opti
By the way, is this ever reviewed:
"Your mail to 'gmx-users' with the subject
Re: [gmx-users] Why does the -append option exist?
Is being held until the list moderator can review it for approval."
On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham
wrote:
> On 4/06/2011
At first, I thought the -append option of the mdrun command was great.
However, I don't think it is anymore and have actually started questioning
myself why it exists at the first place, and second, why has it become the
default option in the newest versions?
It is useless unless you run your sim
On Mon, May 9, 2011 at 1:39 AM, Mark Abraham wrote:
> On 9/05/2011 2:01 PM, Dimitar Pachov wrote:
>
> Hi,
>
> On Sat, May 7, 2011 at 9:45 PM, Justin A. Lemkul wrote:
>
>
>> Please clarify - do you wish to maintain the original triclinic
>> representation (as
Hi,
On Sat, May 7, 2011 at 9:45 PM, Justin A. Lemkul wrote:
> Please clarify - do you wish to maintain the original triclinic
> representation (as -ur tric does) or do you wish to see the octahedral
> representation (as -pbc mol -ur compact gives)? My answer was based on your
> request to "kee
On Sat, May 7, 2011 at 11:02 AM, Justin A. Lemkul wrote:
>
>
> Dimitar Pachov wrote:
>
>> Hello,
>>
>> I have performed simulations of protein+ligands (solute) in truncated
>> octahedral unit cell of waters (solvent). I would like to retain the shape
>>
Hello,
I have performed simulations of protein+ligands (solute) in truncated
octahedral unit cell of waters (solvent). I would like to retain the shape
of unit cell and have the solute centered in such a way as to be completely
surrounded by solvent. At this point, I cannot achieve this although
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