I've just found a solution for this: just need to add flag -res , so the command would be: gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res then choose C-alpha as a group for rms calculation
I've just found a solution for this: just need to add flag -res , so the command would be: gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res then choose C-alpha as a group for rms calculation
I've just found a solution for this: just need to add flag -res , so the command would be: gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res then choose C-alpha as a group for rms calculation
I've just found a solution for this: just need to add flag -res , so the command would be: gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res then choose C-alpha as a group for rms calculation
Generally For atomic level gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg and for residue, you need to flag -res gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg -res
Generally For atomic level gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg and for residue, you need to flag -res gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg -res
You need to use the flag -res, if not the default is measured by atom.
Cheers
You need to use the flag -res, if not the default is measured by atom.
Cheers
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I've just found a solution for this:
just need to add flag -res , so the command would be:
gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res
then choose C-alpha as a group for rms calculation
I've just found a solution for this:
just need to add flag -res , so the command would be:
gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res
then choose C-alpha as a group for rms calculation
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Thank you! M. Florencia Martini
Thank you! M. Florencia Martini
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You have to create an index:
$ gmx make_ndx -f md_0_10.tpr -o index_ca.ndx
Choose
> 1 & 3
22 Protein_&_C-alpha : 347 atoms
Then, calculate RMSF as follows:
gmx rmsf -s md_0_10.tpr -f md_0_10_center.xtc -n index_ca.ndx -o rmsf_protein.xvg
You have to create an index:
$ gmx make_ndx -f md_0_10.tpr -o index_ca.ndx
Choose
> 1 & 3
22 Protein_&_C-alpha : 347 atoms
Then, calculate RMSF as follows:
gmx rmsf -s md_0_10.tpr -f md_0_10_center.xtc -n index_ca.ndx -o rmsf_protein.xvg
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I've just found a solution for this:
just need to add flag -res , so the command would be:
gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res
then choose C-alpha as a group for rms calculation
I've just found a solution for this:
just need to add flag -res , so the command would be:
gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res
then choose C-alpha as a group for rms calculation
More
VOTE
You need to use the flag -res, if not the default is measured by atom.
Cheers
You need to use the flag -res, if not the default is measured by atom.
Cheers
More
VOTE
Generally
For atomic level
gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg
and for residue, you need to flag -res
gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg -res
Generally
For atomic level
gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg
and for residue, you need to flag -res
gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg -res
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VOTE
For atomic level
gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg
and for residue
gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg
change .xtc and .tpr file name accordingly.
For atomic level
gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg
and for residue
gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg
change .xtc and .tpr file name accordingly.
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gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg
gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg
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