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Bilayer self-assembly but with different lipid than in tutorial
- Hryc
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1 year 7 months ago #9501
by Hryc
Bilayer self-assembly but with different lipid than in tutorial was created by Hryc
I did with success "Building self-assembly tutorial"
cgmartini.nl/index.php/tutorials-general...ilayer-self-assembly
but I try to do the same thing with different lipid - monogalactosyldiacylglycerol (DFMG; 18:3), but I have a problem. Sometimes I have an information Warning: pressure scaling more than 1% and my simulation is stopped I tried to change the box size because DFMG probably occupies more volume than DOPC. But I have again this error and sometimes I have error like Step 20 Warning: pressure scaling more than 1%, mu: -2550.14 -2550.14 -2550.14
Warning: Triclinic box is too skewed.
When I have box size=9
I also tried to increase the number of steps in minimization, but It didn't help.
This is my bash script which I use
.mdp files are the same as in the tutorial
What should I do now?
but I try to do the same thing with different lipid - monogalactosyldiacylglycerol (DFMG; 18:3), but I have a problem. Sometimes I have an information Warning: pressure scaling more than 1% and my simulation is stopped I tried to change the box size because DFMG probably occupies more volume than DOPC. But I have again this error and sometimes I have error like Step 20 Warning: pressure scaling more than 1%, mu: -2550.14 -2550.14 -2550.14
Warning: Triclinic box is too skewed.
When I have box size=9
I also tried to increase the number of steps in minimization, but It didn't help.
This is my bash script which I use
#!/bin/bash
box_size=9
nmol=128
radius=0.21
try=500
maxsol=768
radius=0.21
gmx grompp -f minimization.mdp -c DFMG.gro -p dfmg_one_molecule.top
gmx mdrun -deffnm DFMG-em -v
gmx insert-molecules -ci DFMG-em.gro -box $box_size $box_size $box_size -nmol $nmol -radius $radius -try $try -o 128_noW.gro
gmx grompp -f minimization.mdp -c 128_noW.gro -p dfmg_no_water.top -o dfmg-min-init.tpr
gmx mdrun -deffnm dfmg-min-init -v -c 128_minimized.gro
gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol $maxsol -radius $radius
gmx grompp -f minimization.mdp -c waterbox.gro -p dfmg.top -o dfmg-min-solvent.tpr
gmx mdrun -deffnm dfmg-min-solvent -v -c minimized.gro
gmx grompp -f martini_md.mdp -c minimized.gro -p dfmg.top -o dfmg-md.tpr
gmx mdrun -deffnm dfmg-md -v.mdp files are the same as in the tutorial
What should I do now?
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