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freeze dinamics
- Emma
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12 years 6 months ago #796
by Emma
freeze dinamics was created by Emma
hello!
i am doing simulation of a protein in different concentrations of solvents. i am trying to do the simulation in 50%-50% but when i freeze the protein (in order to make a dynamic for solvent equilibration) and do the grompp i get this error:
Fatal error:
[ file freeze3.itp, line 8 ]:
Atom index (7) in position_restraints out of bounds (1-5).
This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
i don't understand why it was working before with other solvent conditions (this is the only difference of the system) and it is not working now...can you explain the error i am making and how can i solve it?
thank you in advance!
Emma
i am doing simulation of a protein in different concentrations of solvents. i am trying to do the simulation in 50%-50% but when i freeze the protein (in order to make a dynamic for solvent equilibration) and do the grompp i get this error:
Fatal error:
[ file freeze3.itp, line 8 ]:
Atom index (7) in position_restraints out of bounds (1-5).
This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
i don't understand why it was working before with other solvent conditions (this is the only difference of the system) and it is not working now...can you explain the error i am making and how can i solve it?
thank you in advance!
Emma
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- djurre
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12 years 6 months ago #797
by djurre
Replied by djurre on topic freeze dinamics
Hey Emma,
Just to get things straight: I guess you mean you are position restraining the protein and not freezing it (that would be by using freeze groups in the mdp file).
Apart from that it is a bit hard to say what is wrong without seeing the topology files. Some checks: The position restraints section has to be directly after the protein specific topology part (for example, [position_restraints] comes directly after the [dihedrals] section.
Just to get things straight: I guess you mean you are position restraining the protein and not freezing it (that would be by using freeze groups in the mdp file).
Apart from that it is a bit hard to say what is wrong without seeing the topology files. Some checks: The position restraints section has to be directly after the protein specific topology part (for example, [position_restraints] comes directly after the [dihedrals] section.
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