Ok, the problem is solved.
Thank you.
Fabio
On 07/27/2011 05:17 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Thanks.
This actually solved the problem in grompp.
I still have problems when running. This is the log of mdrun:
Initializing Domain Decomposition on 4096 nodes
Dynamic load bal
Fabio Affinito wrote:
Thanks.
This actually solved the problem in grompp.
I still have problems when running. This is the log of mdrun:
Initializing Domain Decomposition on 4096 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum int
Thanks.
This actually solved the problem in grompp.
I still have problems when running. This is the log of mdrun:
Initializing Domain Decomposition on 4096 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances
Fabio Affinito wrote:
This is the key part:
processing coordinates...
Warning: atom name 18113 in topol.top and out.gro does not match (MN1
- CN1)
Warning: atom name 18114 in topol.top and out.gro does not match (MN2
- CN2)
Warning: atom name 18115 in topol.top and out.gro does not match (N
On 07/27/2011 04:12 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/27/2011 03:54 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
This is the mdrun output:
Initializing Domain Decomposition on 4096 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (r
Fabio Affinito wrote:
On 07/27/2011 03:54 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
This is the mdrun output:
Initializing Domain Decomposition on 4096 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-grou
On 07/27/2011 03:54 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
This is the mdrun output:
Initializing Domain Decomposition on 4096 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bon
Fabio Affinito wrote:
This is the mdrun output:
Initializing Domain Decomposition on 4096 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 30.031 nm, LJ-14, atoms 407
On 07/27/2011 03:38 PM, Justin A. Lemkul wrote:
Please make sure to keep the discussion on the list.
Sorry, I just was continuing the discussion after sending you my
coordinates.
Fabio Affinito wrote:
Justin,
first of all, I thank you very much for your help: it's very precious.
I regret
Please make sure to keep the discussion on the list.
Fabio Affinito wrote:
Justin,
first of all, I thank you very much for your help: it's very precious. I
regret I didn't notice before the molecule was broken.
I suggested to you yesterday that your initial configuration was broken. You
to
The problem is indeed as I suspected. Your molecules are broken across periodic
boundaries in the initial configuration. When you replicate with genbox, you've
now replicated broken molecules such that those at the new interfaces between
the boxes appear to be intact, but in fact they are no
Fabio Affinito wrote:
On 07/26/2011 07:02 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW
On 07/26/2011 07:02 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0
Fabio Affinito wrote:
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOL HW1 0 13.069 8.987 7.
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0.0638
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOLHW10 13.069 8.987 7.081 0.5916 0.5409 0.0638
Could this be the or
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOLHW10 13.069 8.987 7.081 0.5916 0.5409 0.0638
Could this be the origin of my problem?
Than
Fabio Affinito wrote:
On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not
On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not, depending on what you m
Fabio Affinito wrote:
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's mad
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not, depending on what you mean by "whole".
It is an ion channel, so it's made of four chains.
This cl
Fabio Affinito wrote:
Hi all,
I used genconf because I wanted to replicate a membrane with ion channel
on the xy plane:
genconf -f conf.gro -o out.gro -nbox 2 2 1
Then I edited by hand the .top file where I modified the number of
molecules in the system.
When attempting to run, disregardi
Hi all,
I used genconf because I wanted to replicate a membrane with ion channel
on the xy plane:
genconf -f conf.gro -o out.gro -nbox 2 2 1
Then I edited by hand the .top file where I modified the number of
molecules in the system.
When attempting to run, disregarding the number of processo
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