On 11/2/12 11:08 AM, Albert wrote:
On 11/02/2012 04:02 PM, Justin Lemkul wrote:
I wasn't suggesting that you use NPT, I was merely pointing out that you made
an statement that wasn't true and thought I would mention it.
It looks like you have other issues to deal with.
-Justin
Hello Just
On 11/02/2012 04:02 PM, Justin Lemkul wrote:
I wasn't suggesting that you use NPT, I was merely pointing out that
you made an statement that wasn't true and thought I would mention it.
It looks like you have other issues to deal with.
-Justin
Hello Justin:
thanks a lot for such kind rep
On 11/2/12 10:56 AM, Albert wrote:
On 11/01/2012 06:15 PM, Justin Lemkul wrote:
On 11/1/12 12:55 PM, Albert wrote:
hello:
I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for
16 different temperature with exchange step 300.
Based on your .mdp file, you're not
On 11/01/2012 06:15 PM, Justin Lemkul wrote:
On 11/1/12 12:55 PM, Albert wrote:
hello:
I am running a 40ns REMD with GBSA solvent NPT simulations. It is
exchange for
16 different temperature with exchange step 300.
Based on your .mdp file, you're not doing NPT (pcoupl = no).
Hello J
On 11/1/12 12:55 PM, Albert wrote:
hello:
I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for
16 different temperature with exchange step 300.
Based on your .mdp file, you're not doing NPT (pcoupl = no).
mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb
hello:
I am running a 40ns REMD with GBSA solvent NPT simulations. It is
exchange for 16 different temperature with exchange step 300.
mpiexec -n 384 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s
remd_.tpr -multi 16 -replex 300
I found that it will require 1 months to be finished whi
On 25/04/2012 3:24 PM, Albert wrote:
hello:
it is blue gene P. And the gromacs is single precision in the
cluster. Getting Loaded...And the administrator told me that I have to
use the multiples of 32 in the bg_size parameter. The number specified
in "-np" should be 4 times bg_size.
Yes,
hello:
it is blue gene P. And the gromacs is single precision in the
cluster. Getting Loaded...And the administrator told me that I have to
use the multiples of 32 in the bg_size parameter. The number specified
in "-np" should be 4 times bg_size.
It is even slower than my own workstation
On Tue, 24 Apr 2012 15:42:15 +0200
Albert wrote:
> hello:
>
>I am running a 60,000 atom system with 128 core in a blue gene
> cluster. and it is only 1ns/day here is the script I used for
You don't give any information what exact system that is (L/P/Q?), if
you run single or double pr
On 4/24/12 9:42 AM, Albert wrote:
hello:
I am running a 60,000 atom system with 128 core in a blue gene cluster. and it
is only 1ns/day here is the script I used for submitting jobs:
# @ job_name = gmx_test
# @ class = kdm-large
# @ error = gmx_test.err
# @ output = gmx_test.out
# @ wall_
hello:
I am running a 60,000 atom system with 128 core in a blue gene
cluster. and it is only 1ns/day here is the script I used for
submitting jobs:
# @ job_name = gmx_test
# @ class = kdm-large
# @ error = gmx_test.err
# @ output = gmx_test.out
# @ wall_clock_limit = 00:20:00
# @ job_t
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