[gmx-users] Use NVT to mimic NVE

[Dr. Vitaly Chaban]

Well, if it does not conserve total energy, than such a computational
experiment is not reliable. This is a sad truth.

Philosophically, you have two options here. Either you accept that
energy leakage is significant and then you must fight against it
(smaller time-step, double precision, constraints, etc), or -- on the
contrary -- you say that energy loss can be neglected and proceed "as
is".

My personal rule is if the system does not lose more than 2% of total
energy during an entire run, the result is acceptable. I can be
criticized for this voluntary assumption, obviously.

Anyway, tricks with T-coupling constitute a very bad idea in this
case. You basically try to mask the energy leakage problem with the
thermostat. Thermostat never removes the problem itself.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Sat, Oct 11, 2014 at 11:12 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> I tried NVE on single precision gromacs 4.6.7 with and without GPU.
> The energy either drift down or up, depending on the mdp file, and the drift
> seems linear.
>
> Linear fit says that if I run 100 ns simulation, at the end the energy is
> doubled.
>
> If I use double precision gromacs, the drift seems insignificant over 100 ns
> simulation by linear regression fitting on a 300 ps run.
> But double precision gromacs can't use gpu and is much slower than single
> precision gromacs.
>
> On Sat, Oct 11, 2014 at 4:33 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> wrote:
>>
>> I also cannot get why not to just turn off the thermostat...
>>
>> If energy transfer phenomena are in focus, NVE is an ensemble of
>> choice, no matter which relaxation constant is used for the T-coupling
>> algorithm.
>>
>>
>> Dr. Vitaly V. Chaban
>>
>> Виталий Витальевич ЧАБАН
>>
>>
>> On Sat, Oct 11, 2014 at 6:32 PM, Antonio Baptista <baptista at itqb.unl.pt>
>> wrote:
>> > Then, run true NVE, for the reasons we already pointed.
>> >
>> > On Sat, 11 Oct 2014, Johnny Lu wrote:
>> >
>> >> For dynamics with correct rate and correct fluctuation.
>> >>
>> >> On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban <vvchaban at gmail.com>
>> >> wrote:
>> >>
>> >>> what is it needed for?
>> >>>
>> >>>
>> >>>
>> >>> Dr. Vitaly V. Chaban
>> >>>
>> >>> Виталий Витальевич ЧАБАН
>> >>>
>> >>>
>> >>> On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu <johnny.lu128 at gmail.com>
>> >>> wrote:
>> >>> > Hi.
>> >>> >
>> >>> > Is it a good idea to mimic NVE by a NVT simulation with a large
>> >>> temperature
>> >>> > coupling time constant, to reduce the effect of the thermostat ?
>> >>> >
>> >>> > If I use V-rescale thermostat, what artifacts will the simulation
>> >>> > get
>> >>> > if
>> >>> I
>> >>> > use a large coupling time (say, 500 ps) and single precision gromacs
>> >>> > ?
>> >>> >
>> >>> > Thank you.
>> >>> > --
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