[gmx-users] NPT issue in 4.0.7 and 4.5.3
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Apr 14 08:11:07 CEST 2011
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.
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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