Re: [AMBER] Regarding heating equilibration

From: David A Case <>
Date: Thu, 22 Aug 2019 09:31:00 -0400

On Thu, Aug 22, 2019, Midhun K Madhu wrote:
>I was using AMBER16 (and 18 also) for simulating a protein, lipid water
>system consisting of nearly 100,000 atoms. After energy minimization
>(giving restraints individually on lipid, protein, water and then no
>restraint minimization), I heated the system stepwise to 310K in NVT. But
>when I changed to NPT and restarted the simulations, it shows very high
>energy (very high temperature, sometimes in the range of 1000 K !!!) and
>the simulation stops with an error message 'vlimit exceeds'. I tried to
>continue in NVT, but the case is the same. What could be a possible
>explanation? Can anybody suggest how can I avoid such overheating?

Start with the last "good" NVT restrart file, and run a short (say
100-step) NPT run, setting ntpr=1. Does the energy at the beginning of
the NPT run mostly match that from the end of the NVT run? (There won't
be an exact match, but you should not see any big changes.) Look at the
behavior of the density: what does it start at, how quickly does it

These sort of experiments will help to narrow down the problem.


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Received on Thu Aug 22 2019 - 07:00:02 PDT
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