[gmx-users] NPT issue in 4.0.7 and 4.5.3
Moeed
lecielll at googlemail.com
Thu Apr 14 21:55:02 CEST 2011
On 14 April 2011 02:11, Mark Abraham <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> 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!
:)
>
> 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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