[gmx-users] Constraint and Temperature Drop in NVE

[Johnny Lu]

I try the following:

0. Minimization
1. NVT (100,000 steps of 2fs, 300K)
2. NPT (100,000 steps of 2fs, 300K, V-rescale thermostat)
3. NPT (5000 steps of 2fs, 308K, V-rescale thermostat)
4. 9 x NVE (each 32768 steps of 0.75 fs)
5. go to step 3.

I plan to get rid of the first of nine NVE steps, as an NVE equilibration
step.

At 0.75 fs, the total energy drop was about 0.03% per NVE step.

Will that be fine? I am a bit worry that step 3 is too short.
I pick 308K because last time when I choose 300K for step 3, step 4 drops
to 292 K.
I hope that the NVE will be about 300K.

May be I should look at the .edr file of step 3.

Thanks.


On Wed, Sep 3, 2014 at 11:54 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> reading this post in maillist again:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-May/071225.html
>
> I think that is exactly the same problem.
>
>
> On Wed, Sep 3, 2014 at 10:24 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
>> Hi.
>>
>> After equilibrating with NVT (for 10,000 steps of 2fs) and then NPT
>> (10,000 steps of 2fs with V-rescale thermostat at 300K), when I run NVE
>> (0.5fs timesteps) with a harmonic restraint with force constant 4184kJ/mol
>> rad^2, the temperature then fluctuate around 292 K (
>> http://oi60.tinypic.com/sni5at.jpg) in gromacs 4.6.6.
>>
>> When I instead run NVE with same setting except without the constraint
>> after the two equilibration steps, the temperature stays around 300K.
>>
>> What is the cause of this drop of temperature to 292K?
>>
>> Thanks again.
>>
>>
>>
>