[gmx-users] vacuum simulation vs specific solvent simulation

[Erik Marklund]

Dear Tasneem,

You need to reduce the time step. You are doing NVE simulations, where energy conservation is a bit tricky. You are also not using constraints, which also implies you need to reduce time step. Probably below 0.5 fs. Or you can turn on constraints. We have successfully used LINCS with in NVE vacuum simulations using a 1 fs timestep without significant energy drift in the past (Marklund E G et al (2009) Phys Chem Chem Phys 11, 8069-8078; DOI: 10.1039/B903846A). You may need to increase lincs order and/or iter.

Kind regards,
Erik

> On 7 Sep 2015, at 05:10, tasneem kausar <tasneemkausar12 at gmail.com> wrote:
> 
> Dear users
> 
> Dear gromacs users
> 
> As Joao replied and asked about the purpose of simulation.
> I have performed the vacuum simulation.
> I want to see the secondary structure change in vacuum and in specific
> solvent.
> 
> 
> mdp parameters are :.
> ;
> ;    User spoel (236)
> ;    Wed Nov  3 17:12:44 1993
> ;    Input file
> ;
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  hbonds
> integrator          = steep
> nsteps              =  3000
> ;
> ;    Energy minimizing stuff
> ;
> emtol               =  2000
> emstep              =  0.01
> 
> nstcomm             =  1
> ns_type             =  simple
> rlist               =  0.0
> coulombtype         =  cut-off
> rcoulomb            =  0.0
> rvdw                =  0.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> Tcoupl              =  no
> Pcoupl              =  no
> PBC                 =  no
> gen_vel             =  no
> 
> 
> then i have run the full md for 5ns.
> mdp parameter are as follows:
> 
> ;
> ;    User spoel (236)
> ;    Wed Nov  3 17:12:44 1993
> ;    Input file
> ;
> title               =  Yo
> cpp                 =  /usr/bin/cpp
> constraints         =  hbonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  2500000    ; total 5000 ps.
> nstcomm             =  1
> nstxout             =  500000
> nstvout             =  500000
> comm-mode           =  ANGULAR
> lincs_iter          =  2
> nstfout             =  0
> nstlog              =  500
> nstenergy           =  500
> nstxtcout           =  500
> xtc-precision       =  1000
> nstlist             =  10
> ns_type             =  simple
> rlist               =  0.0
> coulombtype         =  cut-off
> rcoulomb            =  0.0
> rvdw                =  0.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  no
> tc-grps            =  Protein
> tau_t               =  0.1
> ref_t               =  300
> ; Energy monitoring
> energygrps          =  Protein
> ; Isotropic pressure coupling is now on
> Pcoupl              =  no
> Pcoupltype          = isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is off at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> PBC                 =  no
> 
> 
> Am I using the correct mdp parameters for vacuum simulation.
> If anyone know about this, please help...........
> 
> Thanks and reagards
> -- 
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