Commit 76896658 authored by Brandon's avatar Brandon

update namd docs

parent f1d0b77c
#!/bin/bash
#SBATCH --qos=regular
#SBATCH --time=02:00:00
#SBATCH --nodes=100
#SBATCH --nodes=4
#SBATCH --constraint=haswell
#SBATCH --ntasks-per-node=32
#SBATCH --cpus-per-task=2
#SBATCH --switches=1@20
# make sure Haswell environment is loaded
module unload ${CRAY_CPU_TARGET}
module load craype-haswell
# make sure correct hugepages module is loaded
module unload $(module -l list 2>&1 | grep craype-hugepages | awk '{print $1}')
module load craype-hugepages8M
module load rca
module swap craype-${CRAY_CPU_TARGET} craype-haswell
module load namd
export HUGETLB_DEFAULT_PAGE_SIZE=8M
export HUGETLB_MORECORE=no
srun namd2 ${INPUT_FILE}
#!/bin/bash
#SBATCH --qos=regular
#SBATCH --time=02:00:00
#SBATCH --nodes=100
#SBATCH --nodes=8
#SBATCH --constraint=knl
#SBATCH --ntasks-per-node=66
#SBATCH --ntasks-per-node=68
#SBATCH --cpus-per-task=4
#SBATCH --core-spec=2
#SBATCH --switches=1@20
# make sure KNL environment is loaded
module unload ${CRAY_CPU_TARGET}
module load craype-mic-knl
# make sure correct hugepages module is loaded
module unload $(module -l list 2>&1 | grep craype-hugepages | awk '{print $1}')
module load craype-hugepages8M
module load rca
module swap craype-${CRAY_CPU_TARGET} craype-mic-knl
module load namd
export HUGETLB_DEFAULT_PAGE_SIZE=8M
export HUGETLB_MORECORE=no
srun namd2 ${INPUT_FILE}
......@@ -4,7 +4,6 @@
#SBATCH --nodes=10
#SBATCH --ntasks-per-node=24
#SBATCH --cpus-per-task=2
#SBATCH --switches=1@20
# make sure correct hugepages module is loaded
module unload $(module -l list 2>&1 | grep craype-hugepages | awk '{print $1}')
......
# NAMD
[NAMD](www.ks.uiuc.edu/Research/namd/) is a molecular dynamics (MD)
program designed for parallel computation. Full and efficient
treatment of electrostatic and van der Waals interactions are provided
via the (O(N Log N) Particle Mesh Ewald algorithm. NAMD interoperates
with CHARMM and X-PLOR as it uses the same force field and includes a
rich set of MD features (multiple time stepping, constraints, and
dissipatitve dynamics).
program designed for parallel computation.
## Example run script
......@@ -32,5 +27,8 @@ such that *only* the number of nodes needs to be changed.
* [User's Guide](https://www.ks.uiuc.edu/Research/namd/current/ug/)
* [Problem with NAMD?](https://www.ks.uiuc.edu/Research/namd/bugreport.html)
* **IF** after the above you believe there is an issue with the NERSC
module file a ticket with our [help desk](https://help.nersc.gov)
!!! tip
If *after* the checking the above you believe there is an
issue with the NERSC module file a ticket with
our [help desk](https://help.nersc.gov)
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment