[gmx-users] NVT and NVE

[Markus Miettinen]

Hi Jes,


  if you want just to do NVE, it should, in my opinion,
  work also with the Cut-off. But it should also work with
  the Shift, and then your potential will be smooth and
  nice, so this might be the choice you want to take.

  The information given in 7.3.10 is quite cryptic,
  and you can see more about what the different cut-
  offs mean in Gromacs from for example here:

    http://www.gromacs.org/pipermail/gmx-users/2007-July/028626.html

  The bottom line being, though, that if you want to do
  things correct, you set rvdw < rlist. All this wizardry
  with twin range cut-offs and setting rlist < rvdw will
  not work in NVE, because you will not have the thermostat
  to fix the errors done in the integration.


Cheers,
markus.

--
Halli delendum est.

On Apr 7, 2008, at 02:26 , gmx-users-request at gromacs.org wrote:

> Date: 7 Apr 2008 03:52:42 -0000
> From: "JMandumpal" <jesbman at rediffmail.com>
> Subject: Re: Re: Re: [gmx-users] NVT and NVE
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID: <20080407035242.4670.qmail at f4mail-234-117.rediffmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> 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