[gmx-users] NPT issue in 4.0.7 and 4.5.3
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Apr 15 02:02:23 CEST 2011
On 15/04/2011 5:55 AM, Moeed wrote:
>
>
> On 14 April 2011 02:11, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
> On 14/04/2011 3:40 PM, Moeed wrote:
>>
>>
>> On 13 April 2011 18:45, Mark Abraham <Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>
>> On 14/04/2011 10:22 AM, Moeed wrote:
>>> Hello,
>>>
>>> I have run 2 ns simulations on a hydrocarbon system (initial
>>> density of ~ 2 SI and box size is 15 nm), one with version
>>> 4.0.7 and the other trial using 4.5.3. Both runs are almost
>>> equilibrated to 70 bar pressure but one is giving density of
>>> above 600SI (4.0.7) and the other density of around 15 SI
>>> (4.5.3). With 4.5.3 applying 100 bar pressure does not
>>> comrades the system either to the desired density. I need to
>>> study the system at different pressures from 1 to 70 bar,
>>> and I am wondering if the system can not be compressed with
>>> these ref_p values how can I keep the pressure fixed at P <
>>> 70 bar!?
>>>
>>> Please help if you have any idea on why these two versions
>>> are giving inconsistent results and which one is reliable.
>>
>> Why are your potential energies positive? What does the final
>> configuration look like? Why aren't you doing a "simulated
>> annealing" style of compression with small increments of
>> delta-P? (These, coincidentally are even good data for your
>> study...) Massive leaps in ensemble conditions are often
>> poorly-conditioned for numerical integration. You're
>> generating velocities that are only approximately correct,
>> not giving them any chance to equilibrate, and then smashing
>> the system with massive over-pressure. Small wonder it might
>> sometimes break...
>>
>>
>> Hi Mark,
>>
>> You mean I should get negative potential? I am sure topology is
>> generated properly. can you explain why this is concerning?
>
> What does a set of charges with positive potential energy want to do?
>
>
>> Can you please elaborate on compressing using simulated
>> annealing? How can I do this?
>
> That's not what I said - I used quotation marks and the word
> "style" for a reason. I told you not to do massive changes of
> conditions, and to use small increments of delta-P. Equilibrate at
> one P, change it a bit. Repeat. This is like simulated annealing,
> but with P instead of T.
>
>
> Dear Mark,
>
> I see now what you mean. But actually my problem is not equilibrating..
Your problem *is* equilibrating. Clearly 4.5.3 is not doing it.
> I can follow your advise and equilibrate the system but as I said
> starting from the same structure and settings, both runs one with
> 4.0.7 and the other 4.5.3, show that system is pretty close to ref_p =
> 70 but densities are terrible different.
Sure, so something got broken in at least one of these. I think you're
being too rough.
> What I dont realize is that how to judge which version is giving
> correct density. and also version 4.5.3 does not compress with any
> pressure below 100 bar. So even when I compress using 4.0.7, and try
> to use output structure from 4.0.7 as input for 4.5.3 to apply say
> ref_p of 70, my box expands again.
You're trying to draw deductions based on the doubtful premise that you
can just apply a massive overpressure and the numerical integration will
cope. Think about it - massive external pressure means lots of
collisions and large velocities which mean large atomic motions over
finite time steps. You've just left the integration step the same size,
so I'm actually a bit surprised 4.0.7 appears to have coped. A gentler
progressive compression will leave the system close to equilibrium
throughout, and is much more likely to achieve a sensible result.
> I am stuck on this and it seems the only option is to just stick to
> version 4.0.7!
I'm going to stop repeating myself soon :-) I think you're being too
rough, and that 4.5.3 is getting unlucky and breaking and that 4.0.7
might be getting lucky.
Mark
> :)
>
>
> Mark
>
>
>> Thanks, :)
>>
>>
>> When reporting output from .log file and g_energy, please
>> either use plain text email, or switch to a non-proportional
>> font like Courier. Those tables make it harder for people to
>> help you than you want it to be.
>>
>> Mark
>>
>>
>>>
>>> 4.0.7
>>>
>>> Statistics over 250001 steps [*1500.0001 thru 2000.0001 ps
>>> ],* 14 data sets
>>> The term 'Cons. rmsd ()' is averaged over 2501 frames
>>> All other averages are exact over 250001 steps
>>>
>>> Energy Average RMSD
>>> Fluct. Drift Tot-Drift
>>> -------------------------------------------------------------------------------
>>> Angle 36.9945 0.806738 0.804483
>>> 0.0521993 0.208798
>>> Ryckaert-Bell. 9.04227 0.376253 0.371412
>>> 0.0521057 0.208424
>>> LJ-14 5.23048 0.119612 0.119611
>>> 0.00033983 0.00135933
>>> Coulomb-14 -1.66329 0.104171 0.102175
>>> 0.0175753 0.0703015
>>> LJ (SR) -27.3967 0 0
>>> 0.0421934 0.168774
>>> Coulomb (SR) 8.98711 0.163579 0.16062
>>> -0.0268199 -0.10728
>>> Potential 31.1944 0 0
>>> 0.137594 0.550377
>>> Kinetic En. 51.1009 0.987759 0.987724
>>> 0.00725949 0.0290381
>>> Total Energy 82.2953 0 0
>>> 0.144851 0.579408
>>> Temperature 299.98 5.79849 5.79828
>>> 0.000340897 0.170449
>>> *Pressure (bar) 69.3587 414.279 414.256
>>> 0.0298385 14.9193*
>>> Cons. rmsd () 4.01744e-06 1.41883e-07
>>> 1.41883e-07 0 0
>>> *Box-X 3.04882 0 0
>>> 3.57512e-06 0.00178757
>>> Box-Y 3.04882 0 0
>>> 3.57512e-*
>>>
>>>
>>> -----------------------------
>>> 4.5.3.
>>>
>>> [*1500.0001 thru 2000.0001 ps ],*
>>>
>>> Energy Average Err.Est. RMSD
>>> Tot-Drift
>>> -------------------------------------------------------------------------------
>>> Angle 37.1357 0.071 0.812307
>>> -0.099711 (kJ/mol)
>>> Ryckaert-Bell. 9.17677 0.14 0.445934
>>> -0.529281 (kJ/mol)
>>> LJ-14 5.18878 0.0087 0.137673
>>> -0.03119 (kJ/mol)
>>> Coulomb-14 -1.60372 0.051 0.126405
>>> -0.144403 (kJ/mol)
>>> LJ (SR) -4.24478 0.29 0.742141
>>> 0.697187 (kJ/mol)
>>> Coulomb (SR) 8.97451 0.082 0.198278
>>> 0.232025 (kJ/mol)
>>> Potential 54.6272 0.31 1.20733
>>> 0.124627 (kJ/mol)
>>> Kinetic En. 51.1047 0.021 0.9945
>>> -0.066306 (kJ/mol)
>>> Total Energy 105.732 0.31 1.58869
>>> 0.058321 (kJ/mol)
>>> Temperature 300.002 0.12 5.83806
>>> -0.389239 (K)
>>> *Pressure 66.734 5.3
>>> 91.83 11.5294 (bar)*
>>> Constr. rmsd 2.2661e-10 2.3e-10 3.58302e-08
>>> -1.3595e-09 ()
>>> *Box-X 11.0055 0.082 0.175309
>>> -0.496198 (nm)
>>> Box-Y 11.0055 0.082 0.175309
>>> -0.496198 (nm)*
>>>
>>>
>>>
>>>
>>>
>>>
>>> pbc = xyz
>>>
>>> integrator = md
>>> dt = 0.002
>>> nsteps = 1000000
>>> nstcomm = 100
>>> nstenergy = 100
>>> nstxout = 100
>>>
>>> nstlist = 10
>>> ns_type = grid
>>>
>>> coulombtype = Shift
>>> vdw-type = Shift
>>> rcoulomb-switch = 0
>>> rvdw-switch = 0.9
>>> rlist = 1.2
>>> rcoulomb = 1.2
>>> rvdw = 1.0
>>>
>>> Tcoupl = v-rescale
>>> tc-grps = System
>>> tau_t = 0.1
>>> ref_t = 300
>>>
>>>
>>> Pcoupl = berendsen
>>> Pcoupltype = isotropic
>>> tau_p = 1
>>> compressibility = 4.5e-5 4.5e-5
>>> ref_p = 70
>>>
>>>
>>> gen_vel = yes
>>> gen_temp = 300.0
>>> gen_seed = 173529
>>>
>>>
>>> constraints = all-bonds
>>> constraint-algorithm = lincs
>>>
>>
>>
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