Dear David Case,
I use taup=20 for a ~ 2-3 ns duration NPT equilibration at 400K with dt=0.0015 (at 300K, the protein is kinetically trapped, and at 425K, the protein starts unfolding in the lipid bilayer).
For the equilibration phase over 10 ns using a NPgT ensemble, I used taup=1000 at 400K with dt=0.0015, to get the simulation to run without skinnb errors. There was a rather dramatic change in the box dimensions as the bilayer accommodated to the protein. The density continued to increase over 10 ns, so more time is required for a full equilibration. Using 10 fold lesser values of taup would result in skinnb errors, and this cannot be resolved even if multiple restarts were used.
Based on the summary below using a NPgT ensemble, do you think the volume fluctuations are sufficient or too low ?
Thanks
------------------------------------------------------------------------------
A V E R A G E S O V E R 6660 S T E P S
NSTEP = 6660000 TIME(PS) = 11960.000 TEMP(K) = 400.03 PRESS = -117.5
Etot = -67007.0072 EKtot = 65340.2509 EPtot = -132347.2581
BOND = 5588.8650 ANGLE = 20892.1851 DIHED = 15154.3310
1-4 NB = 5215.4696 1-4 EEL = 15874.8516 VDWAALS = 2815.7060
EELEC = -197888.6663 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 18000.5279 VIRIAL = 21069.7800 VOLUME = 1211204.0332
SURFTEN = 10.6531
Density = 0.6218
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 6660000 TIME(PS) = 11960.000 TEMP(K) = 1.37 PRESS = 74.7
Etot = 391.0916 EKtot = 223.4105 EPtot = 321.9510
BOND = 69.6143 ANGLE = 127.1752 DIHED = 67.3018
1-4 NB = 35.0175 1-4 EEL = 64.2282 VDWAALS = 216.9718
EELEC = 376.5890 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 119.4856 VIRIAL = 1941.1697 VOLUME = 36874.9245
SURFTEN = 56.5099
Density = 0.0191
------------------------------------------------------------------------------
On 26 Sep, 2013, at 7:46 PM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Thu, Sep 26, 2013, Wang Chern Hoe (Dr) wrote:
>>
>> My experience indicated that taup had a drastic effect for NPT and NPgT
>> simulations which run into skinnb errors,
>
> Using a large taup slows down the rate at which the box changes size, which
> may appear to help the code respond to such changes. But it also really
> reduces the fluctuations in volume once you have reached the equilibrated
> box size. So, it may make sense to use increase taup during equilibration,
> when you are far from from the correct box size and density, but it seems
> dangerous to use values greater than 1 ps or so for a "production" phase of
> the simulation. (Even a 1ps, volume fluctuations are smaller than they should
> be for a canonical ensemble; we are working on better barostats.)
>
> Caveat: I've not done lipid simulations. As Ross says, there may be some
> other source of your particular problems.
>
> ...dac
>
>
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Received on Thu Sep 26 2013 - 23:30:04 PDT
