On 7/10/14, 7:09 PM, Rasoul Nasiri wrote:
Because 1- Estimation of T for different sub-systems say phases of gas, interface and liquid. Can be obtained with g_energy?
No, not unless they are assigned as separate tc-grps in the .mdp file, but then (1) you shouldn't be designing something affecting the physics purely based on what you hope to analyze and (2) you then already know the outcome.
This is actually what g_traj can do; like I said, you just have to account for restraints.
2- My trajectory is not constrain one as it has been recorded using reactive FF. I need to estimate T with converted trajectory (reaxff---->gro).
Converted trajectory? Your first post suggested the run was done with Gromacs (being that you had .tpr and .edr files). The outcomes you posted agree perfectly with constrained molecules, but without more details on what you're actually doing, I'm not going to hazard a guess. Recall that even if you set "constraints = none," SETTLE is still applied to water molecules unless you use -DFLEXIBLE (which you shouldn't for most normal purposes).
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