REST2 simulations: Corecting shifted dcd files!

From: Bhati, Agastya (agastya.bhati.14_at_ucl.ac.uk)
Date: Wed Oct 11 2017 - 14:36:14 CDT

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Hi,

I have been performing FEP/REST2 simulations using the customised NAMD developed by Sunhwan and Wei (https://doi.org/10.1016/j.cpc.2015.08.030d81XgMvsSgAlE2STw8uHNjiWSde7D6MMI72Rs&e=>). I perform 20 steps of minimisation and 5000 steps of equlibration before attempting the first exchange. Unfortunately, I used the same DCDfile for the entire simulation and a dcdfreq of 5000. This essentially means that I have an additional frame at the beginning of all my dcd files. And the worst part is that the conformations saved in my dcd files are written 20 steps before the exchange attempts. Due to this, the potential energies in my "*.history" files are about 5x times the actual potentials (as in the log files) and the results I get are problematic.

Is there any way to get over this problem by somehow modifying the history files or sorting the dcds differently and get correct results using the existing dcd and history files I have got? I would appreciate any suggestions.

Regards,
Agastya

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