<P>
<BR>
Hi Markus,<BR>
<BR>
It means that I should change cutoff to the Shift, right (manual 7.3.10)<BR>
<BR>
jes<BR>
<BR>
On Sat, 05 Apr 2008 Markus Miettinen wrote :<BR>
>Hi Jes,<BR>
><BR>
><BR>
> to me it seems that you have rlist = rvdw:<BR>
><BR>
>>nstlist = 10<BR>
>>rlist = 1.0<BR>
>>rvdw = 1.0<BR>
><BR>
><BR>
> This will lead to a loss of energy, because between list updates<BR>
> two particles originally at distance, say, 1.01 from each other<BR>
> can easily move within rvdw from each other, but they will not<BR>
> "see" each other until the lists are updated again.<BR>
><BR>
> In other words, you have particles moving within the attractive<BR>
> LJ-potential region without giving them the speed-up that the<BR>
> attractive potential should provide. This mistake equals loss of<BR>
> energy, and becomes apparent in NVE. In NVT the thermostat<BR>
> (artificially!) fixes the energy loss.<BR>
><BR>
> The correct way is to set rlist > rvdw.<BR>
><BR>
><BR>
>Cheers,<BR>
>markus.<BR>
><BR>
>--<BR>
>Halli delendum est.<BR>
><BR>
>On Apr 3, 2008, at 13:00 , gmx-users-request@gromacs.org wrote:<BR>
><BR>
>>Date: 3 Apr 2008 08:12:40 -0000<BR>
>> From: "JMandumpal" <jesbman@rediffmail.com><BR>
>>Subject: Re: Re: [gmx-users] NVT and NVE<BR>
>>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>
>>Message-ID: <20080403081240.1402.qmail@f4mail-234-118.rediffmail.com><BR>
>>Content-Type: text/plain; charset="iso-8859-1"<BR>
>><BR>
>>Dear David,<BR>
>><BR>
>>I post the input file for the NVE run.<BR>
>><BR>
>>I use SHAKE, Would it be better if I use LINCS?<BR>
>><BR>
>>title = NVE<BR>
>>cpp = /usr/bin/cpp<BR>
>>; RUN CONTROL PARAMETERS<BR>
>>integrator = md<BR>
>>; Start time and timestep in ps<BR>
>>tinit = 500<BR>
>>dt = 0.0015;<BR>
>>nsteps = 360000; 540 ps<BR>
>>; For exact run continuation or redoing part of a run<BR>
>>init_step = 0<BR>
>>; number of steps for center of mass motion removal<BR>
>>nstcomm = 1<BR>
>>; group(s) for center of mass motion removal<BR>
>>comm-grps = SOL<BR>
>>; OUTPUT CONTROL OPTIONS<BR>
>>; Output frequency for coords (x), velocities (v) and forces (f)<BR>
>>nstxout = 0<BR>
>>nstvout = 0<BR>
>>nstfout = 0<BR>
>>; Checkpointing helps you continue after crashes<BR>
>>nstcheckpoint = 1000<BR>
>>; Output frequency for energies to log file and energy file<BR>
>>nstlog = 100000<BR>
>>nstenergy = 1000<BR>
>>; Output frequency and precision for xtc file<BR>
>>nstxtcout = 0<BR>
>>xtc-precision = 1000<BR>
>>; select multiple groups. By default all atoms will be written.<BR>
>>; NEIGHBORSEARCHING PARAMETERS<BR>
>>nstlist = 10<BR>
>>; ns algorithm (simple or grid)<BR>
>>ns_type = grid<BR>
>>; Periodic boundary conditions:<BR>
>>pbc = xyz<BR>
>>; nblist cut-off<BR>
>>rlist = 1.0<BR>
>>; OPTIONS FOR ELECTROSTATICS AND VDW<BR>
>>; Method for doing electrostatics<BR>
>>coulombtype = pme<BR>
>>rcoulomb = 1.0<BR>
>>ewald_rtol = 1e-5 ; since erfc(sigma*rcutoff) =ewald_rtol<BR>
>>optimize_fft = yes<BR>
>>; Relative dielectric constant for the medium<BR>
>>epsilon_r = 1 ; for water<BR>
>>; Method for doing Van der Waals<BR>
>>vdw-type = cut-off<BR>
>>rvdw = 1.0<BR>
>>; Spacing for the PME/PPPM FFT grid<BR>
>>fourierspacing = 0.12 ;<BR>
>>; EWALD/PME/PPPM parameters<BR>
>>pme_order = 4<BR>
>>ewald_geometry = 3d<BR>
>>epsilon_surface = 0<BR>
>>; OPTIONS FOR WEAK COUPLING ALGORITHMS<BR>
>>; Temperature coupling<BR>
>>Tcoupl = no<BR>
>>Pcoupl = no<BR>
>>; GENERATE VELOCITIES FOR STARTUP RUN<BR>
>>gen_vel = no<BR>
>>gen-temp = 300<BR>
>>gen-seed = 173529<BR>
>>; OPTIONS FOR BONDS<BR>
>>constraints = all-bonds<BR>
>>constraint_algorithm = shake<BR>
>>shake_tol = 0.0001<BR>
>>morse = no<BR>
>><BR>
>><BR>
>>rgds,<BR>
>>Jes<BR>
</P>
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