[gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations
jampani srinivas
jampanis at gmail.com
Mon Apr 26 16:20:49 CEST 2010
Dear Berk,
Yes the system is stable and the small velocity appears only at step 0 as
you said.
This looks fine now, Thanks a lot for you continuous support
Thanks very much.
Srinivas.
On Mon, Apr 26, 2010 at 7:43 AM, Berk Hess <gmx3 at hotmail.com> wrote:
> Hi,
>
> So the system seems to be stable now?
>
> The water molecules might get a very small velocity, because constraints
> are always applied.
> If your starting coordinates do not have full precision (e.g. gro or pdb),
> a minor correction
> and thus velocity will occur at step 0 only. This should not be an issue.
>
> Berk
>
> ------------------------------
> Date: Sun, 25 Apr 2010 11:59:36 -0400
>
> Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve
> simiulations
> From: jampanis at gmail.com
> To: gmx-users at gromacs.org
>
> Dear Berk,
>
> First of all thanks very much for your kind patience and help. As a new
> user i am facing some problems and not clear about many options and how to
> use them. I was reading several messages of yours from mailing list which
> are very close to my problem.
> After reading several of them from mailing list i have carefully tuned my
> md.mdp file and the energy out put from g_energy is here.
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++
>
> Last energy frame read 1000 time 2000.000
>
> Statistics over 1000001 steps [ 0.0000 thru 2000.0001 ps ], 1 data sets
> All averages are exact over 1000001 steps
>
> Energy Average RMSD Fluct. Drift
> Tot-Drift
>
> -------------------------------------------------------------------------------
> Total Energy -55074.6 348.391 347.979 -0.0293271
> -58.6543
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> Energy looks pretty stable compare to the one i have reported in Bugzilla,
> in which i always use to get the drift from 200 to 600, and finally it ends
> up with positive energy.
>
> Here is the md.mdp file i have used for my current simulation.
>
> ++++++++++++++++++++++++++++++++++++++++++++
> title = AB2130
> cpp = /usr/bin/cpp
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 1000000 ; total 100.0 ns.
> nstxout = 1000 ; collect data every 2.0 ps
> nstvout = 1000 ; collect velocity every 2.0 ps
> nstfout = 0
> nstlog = 0
> comm_mode = none
> nstenergy = 1000 ; collect energy every 2.0 ps
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 1.0
> coulombtype = cut-off
> rcoulomb = 1.0
> rvdw = 1.0
> rvdw_switch = 0.9
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = V-rescale
> tau_t = 0.1 0.1
> tc-grps = Tmp1 Tmp2
> ref_t = 283.0 0.0
> ;Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 283.0
> energygrps = Tmp1 Tmp2
> energygrp_excl = Tmp2 Tmp2 Tmp2 Tmp1
> gen_seed = 181726
> freezegrps = Tmp2
> freezedim = Y Y Y
> +++++++++++++++++++++++++++++++++++++++++++++++
>
> I still have small question here, when i try to print the velocities from
> trajectory i found that some of the frozen water too get the velocities (i
> have complied my gromcas with md.c
> Fixed velocity output at first step on nodes>1 with PD and frozen groups).
>
> Here is the example for few frozen water.
>
> ++++++++++++++++++++++++++++++++++++++++++++++
> 48SOL OW 149 1.630 1.491 6.061 -0.0001 -0.0000 -0.0000
> 48SOL HW1 150 1.555 1.541 6.027 -0.0001 0.0001 -0.0000
> .
> .
> .
> 9503SOL OW31669 6.075 6.430 0.097 0.0001 0.0000 -0.0000
> 9503SOL HW131670 5.984 6.437 0.126 0.0000 0.0001 -0.0000
> 9503SOL HW231671 6.089 6.508 0.044 -0.0001 0.0001 -0.0000
> ++++++++++++++++++++++++++++++++++++++++++++++++++
>
> I am not very clear why i am still getting this velocity, and how would
> these velocities to frozen atoms effect the simulation?
>
> Can you please give me your suggestions.
>
> Thanks in advance
> Srinivas.
>
>
> --
> *********************************************
> J. Srinivasa Rao
> Post-doctoral Research Associate
> C/o Prof. Luis R Cruz Cruz
> Computational Biophysics Group
> Department of Physics
> Drexel University
> 3141 Chestnut St
> Philadelphia, PA 19104, USA.
> Ph: Off: 215-895-1989
> Mob: 704-706-4191
> **********************************************
>
>
>
> ------------------------------
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--
*********************************************
J. Srinivasa Rao
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph: Off: 215-895-1989
Mob: 704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx
**********************************************
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