#!/bin/bash

​

#SBATCH --job-name=cpprmsd

#SBATCH -N 1

#SBATCH -n 20

##SBATCH --gres=gpu:1

#SBATCH --partition=shortq7,mediumq7,longq7,shortq7-gpu,longq7-rna

##SBATCH --partition=longq7-rna

##SBATCH --mail-type=ALL

#SBATCH --time=6:00:00

##SBATCH --exclusive

##SBATCH --nodelist=nodegpu025

​

​

###################################

#load amber 18 on atlas

###################################

source /opt/ohpc/pub/apps/rnachem/amber18_gpu/amber.sh

source /opt/ohpc/pub/apps/rnachem/amber18_gpu/modules2load.txt

​

rm rmsd*.agr

rm rmsd*.dat

rm first.pdb last.pdb

​

find $SLURM_SUBMIT_DIR -maxdepth 1 -type f \( -name "slurm-*" ! -name "slurm-$SLURM_JOB_ID.out" \) -delete

​

cat>input<<EOF

parm ./strip.prmtop.new

trajin ./combined_md.mdcrd

​

reference resname.pdb

​

symmrmsd AlltoAll :1-14&!@H= reference out rmsd2.agr mass time 0.00002 xlabel "  "

symmrmsd HairpinToHairpin :5-10&!@H= reference out rmsd2.agr mass time 0.00002

symmrmsd StemToStem :1-4,11-14&!@H= reference out rmsd2.agr mass time 0.00002

​

​

symmrmsd AlltoAll2 :1-14&!@H= reference out rmsdAtoA.dat mass time 0.00002 xlabel "  "

symmrmsd HairpinToHairpin2 :5-10&!@H= reference out rmsdHtoH.agr mass time 0.00002

symmrmsd StemToStem2 :1-4,11-14&!@H= reference out rmsdStoS.agr mass time 0.00002

​

# no ref structures

#symmrmsd ToFirstAll1-12 :1-12&!@H= first out rmsd1.agr mass time 0.00002 xlabel "  "

#symmrmsd ToFirstHairpin5-8 :5-8&!@H= first out rmsd1.agr mass time 0.00002

#symmrmsd ToFirstStem1-4,9-12 :1-4,8-12&!@H= first out rmsd1.agr mass time 0.00002

​

#symmrmsd ToFirstAll :1-12&!@H= first out rmsdAll.dat mass time 0.00002

#symmrmsd ToFirstHairpin :5-8&!@H= first out rmsdHairpin.dat mass time 0.00002

#symmrmsd ToFirstStem :1-4,8-12&!@H= first out rmsdStem.dat mass time 0.00002

​

​

run

EOF

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mpirun -n 20 cpptraj.MPI -i input

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############################

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cat>input2<<EOF

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parm ./strip.prmtop.new

trajin ./combined_md.mdcrd 1 1

trajout first.pdb pdb

run

EOF

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cpptraj -i input2

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############################

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cat>input3<<EOF

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parm ./strip.prmtop.new

trajin ./combined_md.mdcrd lastframe

trajout last.pdb pdb

run

EOF

​

​

cpptraj -i input3

​

​

​