[gmx-users] NPT issue in 4.0.7 and 4.5.3
Moeed
lecielll at googlemail.com
Thu Apr 14 07:40:54 CEST 2011
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?
Can you please elaborate on compressing using simulated annealing? How can I
do this?
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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