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about density of the system after genbox
- exianshine
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12 years 3 months ago #900
by exianshine
about density of the system after genbox was created by exianshine
After the genbox step in the " Protein in water" tutorial
the output give the density of the system is about 2g/L. which seems not proper for water in protein.
is it a bug of martini forcefield or my problem?
Thanks for any reply.
the input is :
genbox_mpi -cp ***.gro -cs ../files/water.gro -ci **.gro -nmol 100 -vdwd 0.21 -o ***.gro
the ouotput said:
Added 100 molecules (out of 100 requested) of SDS
Generated solvent containing 20070 atoms in 20070 residues
Writing generated configuration to ASW_box14.gro
Martini system from 1rc2_pH7_label.pdb
Output configuration contains 22366 atoms in 21094 residues
Volume : 2744 (nm^3)
Density : 2269.42 (g/l)
Number of SOL molecules: 0
the output give the density of the system is about 2g/L. which seems not proper for water in protein.
is it a bug of martini forcefield or my problem?
Thanks for any reply.
the input is :
genbox_mpi -cp ***.gro -cs ../files/water.gro -ci **.gro -nmol 100 -vdwd 0.21 -o ***.gro
the ouotput said:
Added 100 molecules (out of 100 requested) of SDS
Generated solvent containing 20070 atoms in 20070 residues
Writing generated configuration to ASW_box14.gro
Martini system from 1rc2_pH7_label.pdb
Output configuration contains 22366 atoms in 21094 residues
Volume : 2744 (nm^3)
Density : 2269.42 (g/l)
Number of SOL molecules: 0
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- djurre
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12 years 3 months ago #901
by djurre
Replied by djurre on topic about density of the system after genbox
The Martini forcefield should give approximately the right density. The output of genbox states that the density is 2269.42 (g/l), very different from 2g/L. I don't know how either of the values is calculated.
However, given that you have 20070 waters, a 924 residue protein and 100 SDS molecules in a 2744nm3 box, the density sounds right (20070 waters * 72 AMU / 2744 nm3 * 1.66 = 874.186 gr/l, where 1.66 is conversion from AMU/nm3 to gr/l. I you take in to account the protein and the SDS the water density will be close to 1000gr/l.)
However, given that you have 20070 waters, a 924 residue protein and 100 SDS molecules in a 2744nm3 box, the density sounds right (20070 waters * 72 AMU / 2744 nm3 * 1.66 = 874.186 gr/l, where 1.66 is conversion from AMU/nm3 to gr/l. I you take in to account the protein and the SDS the water density will be close to 1000gr/l.)
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- exianshine
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12 years 3 months ago #902
by exianshine
Replied by exianshine on topic about density of the system after genbox
thanks for your reply.
as you pointed out, it seems that the genbox gives the wrong calculation.
as you pointed out, it seems that the genbox gives the wrong calculation.
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