Hi all
I apologize if these are boring basic questions but I would really like to get help with them! 1) I´m doing NPT MD simulations of protein in water and got somewhat confused when using tpbconv to restart after the first run. The run is 6million timesteps and nstenergy is set to 250 which I guess should give me 24000 energy outputs to the .edr file. However, my edr file contains 24098 outputs, with an extra output roughly every 58000 timesteps. Why? The log file and trajectory contains the number of outputs I´ve specified and the run did not crash or anything. 2) When restarting with tpbconv I submit the energyfile on the commandline as well as the .trr file. Tpbconv seems to take the last coordinates and velocities from the .trr but not the last frame from the .edr file. This seems to happen also for .edr without the extra frames described above. I have to manually remove all but the last frame from the .edr to have tpbconv select the energy data from the same time as the coordinates. Why? 3) I run Nose-Hoover temperature coupling on the protein and solvent in separate tc_groups, with a ref_t of 350K and tau_t of 0.5. Looking at the protein temperature, it fluctuates from 325K to 375K which to me sounds like a lot, even though the protein is rather small 100residues. The water fluctuates roughly 15K . I do get the warning of less than 10% of the atoms (system size 23000atoms) during grompping. Would it be better to have only one tc_group? Regards /Matteus Matteus Lindgren Graduate student Department of Chemistry Umeå University SE-901 87 Umeå, Sweden Tel: +46 (0)90 786 53 68 e-mail: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
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