[gmx-users] Re: gmx-users Digest, Vol 39, Issue 56
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jul 17 14:24:29 CEST 2007
ann rose wrote:
> ------------------------------
>
> Message: 5
> Date: Mon, 16 Jul 2007 16:39:29 +0200
> From: "Jeroen van Bemmelen" < J.J.M.vanBemmelen at tnw.tudelft.nl
> <mailto:J.J.M.vanBemmelen at tnw.tudelft.nl>>
> Subject: [gmx-users] Regarding polymer equillibration (pressure
> changes)
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID: <
> 469B9F40.30804.32BEF5D at J.J.M.vanBemmelen.tnw.tudelft.nl
> <mailto: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?
Try doing it on a piece of paper: since it is an NVT sim density is
constant.
>
> 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?
>
they are, always. PBC.
>
>
>
>
> Thanking you in advance
>
>
> ------------------------------------------------------------------------
>
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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