[gmx-users] NVT and NVE

[JMandumpal]

Hi Markus,

It means that I should change cutoff to the Shift, right (manual 7.3.10)

jes

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