[gmx-users] Re: gmx-users Digest, Vol 39, Issue 56
ann rose
annrose.johns at gmail.com
Tue Jul 17 14:13:13 CEST 2007
>
> ------------------------------
>
> Message: 5
> Date: Mon, 16 Jul 2007 16:39:29 +0200
> From: "Jeroen van Bemmelen" < J.J.M.vanBemmelen at tnw.tudelft.nl>
> Subject: [gmx-users] Regarding polymer equillibration (pressure
> changes)
> To: gmx-users at gromacs.org
> Message-ID: < 469B9F40.30804.32BEF5D at J.J.M.vanBemmelen.tnw.tudelft.nl>
> Content-Type: text/plain; charset=US-ASCII
>
> Hi Ann,
>
> > So my first question is
> >
> > wether this can be possible or not? or am I doing something wrong?
> > if so, then how can i rectify the same error?
>
> I think you should definitely use 'editconf -density' to rescale your
> simulation box to the right density. editconf automatically rescales
> the box vectors AND the coordinates, so you won't have the problem of
> atom coordinates suddenly being larger than the box vectors.
>
> But anyhow it seems a bit weird to me that you're coordinates are so
> much larger than your box vectors (4.3 versus 3.4 nm). Perhaps this
> is related to the long molecule chains in combination with pbc? I'm
> not sure, maybe one of the developers can comment on this.
>
>
> > I think the fluctuations are okay and admittable.but the change in
> pressure
> > averages make me confused.
> >
> > If I am right, at equillibrium all the observables (temp, pressure,
> density)
> > should average around a steady value with some fluctuations. but the
> change
> > in averages (pressure) makes me confused. I have read from literature
> that
> > the equillibriation of polymers is comparitively diffcult.
>
> Fluctuations in the average pressure do not necessarily mean there's
> a equilibration problem, depending on the time it takes for the
> average pressure to converge for your system. Simply a matter of
> statistics.
>
> Since the pressure is always fluctuating enormously and converging
> slowly compared to other observables, I don't think that (only)
> checking the average pressure is a good way of determining whether a
> system is equilibrated or not. Of course, a drift in the average
> pressure could mean that your system is not equilibrated. But in that
> case you'd probably also see a significantly large drift in other
> observables, especially the potential energy and partial potential
> energy terms in your case.
>
> Cheers,
> Jeroen
Hi jeroen
Thank you for the reply. I forgot to mention the avergae potential , kinetic
and total energy for the simulation runs are as follows
###############################################################################################################
5ns NPT simulation
Last frame read 10000 time 5000.000
Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 1 data sets
Energy Average RMSD Fluct.
Drift Tot-Drift
------------------------------
-------------------------------------------------
Total-Energy 4331.96 355.493 355.355 0.00685523
34.2761
Potential energy -9401.33 250.37 250.31 0.00378263
18.9132
Kinetic energy 13733.3 235.6 235.558 0.0030726
15.363
Pressure 10.4371 724.216 724.216 -8.51094e-05 -
0.425347
Temperature 450 7.71993 7.71856 0.0010068
34.2761
Density 916.781 6.60382 6.60252 9.09303e-05
0.454652
##################################################################################################
5ns NVT simulation
Last frame read 10000 time 5000.000
Statistics over 5000001 steps [ 0.0000 thru 5000.0000 ps ], 1 data sets
Energy Average RMSD Fluct.
Drift Tot-Drift
-------------------------------------------------------------------------------
Total-Energy 4335.29 352.244 351.929 0.0103137
51.5683
Potential energy -9397.99 244.804 244.693 0.00509701
25.4881
Kinetic energy 13733.3 236.317 236.197 0.00521605
26.0803
Pressure 18.06 802.822 802.807 -0.00349252 -
17.4726
Temperature 450 7.74343 7.7395 0.000170915
0.854575
Density 927.262 (g_density -f traj.xtc -s ppo.tpr -sl 1)
#######################################################################################################
10ns NVT simulation
Energy Average RMSD Fluct.
Drift Tot-Drift
-------------------------------------------------------------------------------
Total-Energy 4339.31 350.971 350.812 -0.00732073 -
36.6037
Potential energy -9393.97 244.091 243.963 -0.0054728 -
27.3624
Kinetic energy 13733.3 236.317 236.197 0.00521605
26.0803
Pressure 28.5734 801.629 801.56 0.00729491
39.4746
Temperature 450 7.73025 7.72976 -6.05616e-05 -
0.302808
Density 927.263 (g_density -f traj.xtc -s ppo.tpr -sl 1)
########################################################################################################
The above mentioned are the averages for the system in the cubical box where
the coordinates have vallues greater than the box length.
One of my question was left unanswered regarding the calculation of density.
1.Can i use (g_density -f traj.xtc -s ppo.tpr -sl 1) to calculate the
density of the system in NVT simulation? are the options correct to
calculate the density?
2. When I view the trajectories (ngmx -f traj.xtc -s top.tpr) of my run i
always found my polymer chains hanging out of the box.Is it the periodic
boundary condition that i observe in veiwing the trajectory? (as i mentioned
before some of my cordinates are greater than box length). is that can be
the reason for the same?
3. How can i keep all my molecules inside the box during the simulation run?
Thanking you in advance
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