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Martini Polymer (Tutorial)
- subhamoy
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7 years 4 months ago #6615
by subhamoy
Martini Polymer (Tutorial) was created by subhamoy
Hello,
I have followed the tutorial and could generate the bond and angle distribution for PEG 9. I could even match the free energy calculation in melt, but could not match the solvation free energy in water, following the tutorial ( I can be following it wrong but I have checked multiple times). The solvation free energy in atomistic case is 2.81kJ/mol, while I am getting solvation free energy around 40kJ/mol. I have used GROMACS' g_bar to calculate both of the values from dhdl.xvg files.
I have used SP1 for C-O-H and SN0 for C-O-C for which I got 45.63kJ/mol, when I used SP5-SN0 I got 54.92kJ/mol. If I am not wrong shouldn't the solvation free energy reduce for using a more polar bead? I was hoping to get a possible solution ( Bead types and bonded parameters ) if available, or maybe at least point me in the right direction.
Thank you in advance and sorry if the question is too basic.
I have followed the tutorial and could generate the bond and angle distribution for PEG 9. I could even match the free energy calculation in melt, but could not match the solvation free energy in water, following the tutorial ( I can be following it wrong but I have checked multiple times). The solvation free energy in atomistic case is 2.81kJ/mol, while I am getting solvation free energy around 40kJ/mol. I have used GROMACS' g_bar to calculate both of the values from dhdl.xvg files.
I have used SP1 for C-O-H and SN0 for C-O-C for which I got 45.63kJ/mol, when I used SP5-SN0 I got 54.92kJ/mol. If I am not wrong shouldn't the solvation free energy reduce for using a more polar bead? I was hoping to get a possible solution ( Bead types and bonded parameters ) if available, or maybe at least point me in the right direction.
Thank you in advance and sorry if the question is too basic.
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- riccardo
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7 years 3 months ago #6983
by riccardo
Replied by riccardo on topic Martini Polymer (Tutorial)
Hi subhamoy,
In general, within Martini, solvation free energies are not in such a good agreement with experimental ones as partitioning free energies are (see 2007 SJ Marrink et al JPCB, Table 3). So, the solvation free energy in water you're getting may be okay. Have you computed and compared to published data (see Lee and Rossi works referenced in the tutorial) Martini partitioning free energies for PEG?
Regarding the beads. An SP5 bead interacts more than an SP1 one with water, i.e., (S)P5 - P4 interaction level O (5.6 kJ/mol) vs (S)P1 - P4 interaction level II (4.5 kJ/mol) (interaction matrix Table 1, 2007 SJ Marrink et al JPCB). As a consequence, the interaction between SP5-SN0 and water will be stronger than the interaction of SP1-SNO and water.
I assume you're computing the solvation free energy with TI by switching off the interaction between the 2 beads molecule and water. Like this you're getting a positive deltaG which is the opposite of a solvation free energy (the molecule goes from water --> vacuum). The solvation free energy is -45.63 kJ/mol (the molecule goes from vaccum --> water) in the SP1-SN0 case to -54.92 kJ/mol in the SP5-SN0 case.
In general, within Martini, solvation free energies are not in such a good agreement with experimental ones as partitioning free energies are (see 2007 SJ Marrink et al JPCB, Table 3). So, the solvation free energy in water you're getting may be okay. Have you computed and compared to published data (see Lee and Rossi works referenced in the tutorial) Martini partitioning free energies for PEG?
Regarding the beads. An SP5 bead interacts more than an SP1 one with water, i.e., (S)P5 - P4 interaction level O (5.6 kJ/mol) vs (S)P1 - P4 interaction level II (4.5 kJ/mol) (interaction matrix Table 1, 2007 SJ Marrink et al JPCB). As a consequence, the interaction between SP5-SN0 and water will be stronger than the interaction of SP1-SNO and water.
I assume you're computing the solvation free energy with TI by switching off the interaction between the 2 beads molecule and water. Like this you're getting a positive deltaG which is the opposite of a solvation free energy (the molecule goes from water --> vacuum). The solvation free energy is -45.63 kJ/mol (the molecule goes from vaccum --> water) in the SP1-SN0 case to -54.92 kJ/mol in the SP5-SN0 case.
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