Problem in frame-*_run-umbrella.sh

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question I completed generation of frames for umbrella but when I run the bash frame-*_run-umbrella.sh script only the first frame npt and md are running after which it stops. But according to script all frames should run in loop automatically. What could be the possible solution.

2

could you please share the script here .

3

Screenshot_2024-04-25-21-49-27-336_com.google.android.apps.docs
Screenshot_2024-04-25-21-49-27-336_com.google.android.apps.docs1080×2246 144 KB

4

you should use for loop like this example:

XX=0

for i in $(seq 1 100);
do
    XX=$(expr $XX + 1)
    gmx grompp -f md.mdp -c confXX.gro etc
done
5

Hello, thank for your kind support, actually i am not good in scripting and this script is already given in the tutorial of umbrella gromacs. Therefore can u please help me withi the complete script for this.

6

just add whatever you wanted to run instead of
gmx grompp -f md.mdp -c confXX.gro etc
in the code i provided above.

7

hello, I tried to change the script as suggested but still it did not run in loop , as it again stopped after one sampling.

#!/bin/bash

XX=0

for i in (seq 1 100); do XX=(expr $XX + 1)

Short equilibration

gmx grompp -f npt_umbrella.mdp -c confXXX.gro -r confXXX.gro -p topol.top -n index.ndx -o nptXXX.tpr -maxwarn 4
gmx mdrun -v -deffnm nptXXX

Umbrella run

gmx grompp -f md_umbrella.mdp -c nptXXX.gro -r nptXXX.gro -t nptXXX.cpt -p topol.top -n index.ndx -o umbrellaXXX.tpr -maxwarn 4
gmx mdrun -v -deffnm umbrellaXXX
done

8

run-umbrella
run-umbrella1177×361 6.49 KB

script not worked in loop

9

The code example above was more of an outline, I think, not the exact code that should be used. The variable expansion (XXX should not just be written explicitly) was missing. Something like:

#!/bin/bash

for XXX in {0..100}
do
  # Short equilibration
  gmx grompp -f npt_umbrella.mdp -c conf${XXX}.gro -r conf${XXX}.gro -p topol.top -n index.ndx -o npt${XXX}.tpr -maxwarn 4
  gmx mdrun -v -deffnm npt${XXX} -cpi
  # Umbrella run
  gmx grompp -f md_umbrella.mdp -c npt${XXX}.gro -r npt${XXX}.gro -t npt${XXX}.cpt -p topol.top -n index.ndx -o umbrella${XXX}.tpr -maxwarn 4
  gmx mdrun -v -deffnm umbrella${XXX} -cpi
done

should hopefully work. But you might want separate subdirectories for your simulations instead.

10

Thank you very much sir, my problem is resolved.