[gmx-users] NPT issue in 4.0.7 and 4.5.3
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 14 23:44:00 CEST 2011
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..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. 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.
>
> I am stuck on this and it seems the only option is to just stick to
> version 4.0.7!
>
Upgrade to version 4.5.4. There was a bug involving the output of
pressure-related terms that was fixed. This may or may not be relevant, but
before making such conclusions, always verify your conclusions with the latest
bugfix release.
-Justin
> :)
>
>
> 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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>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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