[gmx-users] Re: enery conserving problem in NVE simulations with SMW4-NPD polarizable force field

[S. Alireza Bagherzadeh]

On Mon, Jul 15, 2013 at 3:00 AM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
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>    1. Re: How to calculate enthalpy (Dr. Vitaly Chaban)
>    2. enery conserving problem in NVE simulations with SMW4-NPD
>       polarizable force field (Ding  Yun)
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 15 Jul 2013 09:43:38 +0000
> From: "Ding  Yun" <yun.ding at phys.chem.ethz.ch>
> Subject: [gmx-users] enery conserving problem in NVE simulations with
>         SMW4-NPD polarizable force field
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID: <E82F84D319900F4CA5FCF4B9BB98716C162426B1 at MBX23.d.ethz.ch>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I'm trying to simulate liquid water (512 water molecules) with SMW4-NPD
> polarizable force field. The NVT simulation looks fine, but when I restart
> it with NVE runs, the total energy of the system keeps drifting down.
>
>  The time step I'm using now is 0.5 fs and emtol=0.01 kJ/mol/nm. Gromacs
> is also compiled with double precision.  Does anyone have any suggestions
> for this kind of problem? Thanks a lot.
>
> Regards,
> Yun
>
>
> My .mdp file:
>
> ; RUN CONTROL PARAMETERS
> integrator               = md
> tinit                    = 800
> init_step                =0
> dt                       = 0.0005 ; time step (ps)
> nsteps                   = 400000  ; number of steps
>
> ; OUTPUT CONTROL OPTIONS
> nstenergy                = 100
> nstxout                  =100
>
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist                  = -1
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.24
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype              = PME-Switch
> rcoulomb                 = 1.05
> rcoulomb_switch          = 0.85
> vdw-type                 = shift
> rvdw                     = 1.05
> ewald_rtol               =1e-4
>
>
> ; OPTIONS FOR BONDS
> constraints              = h-bonds
> ; Type of constraint algorithm
> constraint-algorithm     = Lincs
>
>
> ; Polarizable model parameters
> emtol = 0.01
> niter = 20
>
> ; Temperature coupling
> tcoupl                   = no
>
> ; pressure coupling
>
> pcoupl                = no
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel                  = no
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 111, Issue 69
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>



Try the following for "options for bonds".
constraint-algorithm     = shake
shake-tol                = 1e-10



I hope this helps.

-- 
*S. Alireza Bagherzadeh, M.A.Sc. <https://circle.ubc.ca/handle/2429/26269>
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*PhD Candidate
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