Hello,
I have two questions regarding Gromacs.
I simulate at the moment Polyacrylic Acid in water using the GROMOS 53a6 Force Field.
In the standard force field, the option gen-pairs is set to "no" and also, in the paper they did not say anything about pairs.
So I set nrexcl to 3 because I have dihedrals and they should not be disturbed from the nonbonded interactions and also, I did not define any pairs.
My question here is, is that right or false and if false, why?
Regarding the temperature coupling, I see some peaks at the equilibration of the system, is that normal? And if not what could be wrong?
Best regards,
Tobias
1. Try various temperature couplings and see if they are any differences.
2. In my understanding, fluctuations do occur: please try to extend your simulations to at least 5 nano second to see these three points of fluctuations do remain.
3. You may have to define pairs ( I think you may have to manually add these pairs since your system is relatively small). In articles authors generally do NOT mention about pairs.
Each of the peaks could be caused by a single "hot" (hydrogen?) atom (if the bonds involving hydrogen atoms are not restrained---in the early stages of the equilibrating MD simulation).
My equilibrating MD simulations are typically about 200 ps. i have run > 500 equilibrating MD simulations of proteins, nucleic acids, and their complexes: never longer than about 800 ps.
(i'm not a Gromacs user.)
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