[gmx-users] constant pressure in NPT simulation

[Alex]

Yup. Didn't even notice.

On Mon, Aug 6, 2018, 12:50 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/6/18 9:07 AM, Lucia Mydlova wrote:
> > Thank you very much for your helpful advice.
> >
> > I simulated polymer PMMA with two organic chromophores in NVT ensemble
> for
> > 2ns and, the same system one more time for 1.5ns
> > with parameters:
> > constraints         =  none
> > integrator          =  md
> > dt                  =  0.001
> > nsteps              =  1500000
> > comm_mode           =  Linear
> > nstcomm             =  1
> > nstxout             =  1000
> > nstvout             =  1000
> > nstfout             =  1000
> > nstlog              =  1000
> > nstenergy           =  1000
> > nstxtcout           =  1000
> > xtc_precision       =  1000
> > pbc                 =  xyz
> > nstlist             =  1
> > cutoff-scheme       =  group
> > ns_type             =  grid
> > coulombtype         =  Cut-off
> > vdwtype             =  Cut-off
> > rlist               =  1.10
> > rcoulomb            =  1.10
> > rvdw                =  1.10
> > tcoupl              =  nose-hoover
> > tc_grps             =  system
> > tau_t               =  0.02
> > ref_t               =  300
> > nsttcouple          =  1
> >
> > and now I want to simulate the system in NPT ensemble for different
> > temperature from 100K up to 700K
> > integrator          =  md
> > dt                  =  0.001 ; ps !
> > nsteps              =  2000000
> > comm_mode           =  Linear
> > nstcomm             =  1
> > nstxout             =  1000
> > nstvout             =  1000
> > nstfout             =  1000
> > nstlog              =  1000
> > nstenergy           =  1000
> > nstxtcout           =  1000
> > xtc_precision       =  1000
> > nstlist             =  1
> > cutoff-scheme       =  group
> > ns_type             =  grid
> > pbc                 =  xyz
> > coulombtype         =  Cut-off
>
> A plain cutoff for electrostatic interactions is horribly inaccurate and
> not generally viewed as acceptable for modern simulations.
>
> -Justin
>
> > vdwtype             =  Cut-off
> > rlist               =  1.1
> > rcoulomb            =  1.1
> > rvdw                =  1.1
> > tcoupl              =  nose-hoover
> > tc_grps             =  system
> > tau_t               =  0.02
> > ref_t               =  100
> > Pcoupl              =  Parrinello-Rahman
> > pcoupltype          =  isotropic
> > tau_p               =  1.0
> > compressibility     =  4.5e-5
> > ref_p               =  1.0
> >
> > The fluctuation of pressure is high in simulations. Should I use the same
> > barostat for my system?
> >
> > Lucia
> >
> >
> > 2018-08-03 9:14 GMT+02:00 Lucia Mydlova <lucia.mydlova at gmail.com>:
> >
> >> Dear all customers.
> >>
> >> I have a problem, in my NPT simulations the pressure is not constant and
> >> the temperature is. Earlier simulation in NVT conditions was ok. I use
> >> these parameters:
> >>   tcoupl              =  nose-hoover
> >> tc_grps             =  system
> >> tau_t               =  0.002
> >> ref_t               =  500
> >> Pcoupl              =  parrinello-rahman
> >> pcoupltype          =  isotropic
> >> tau_p               =  1.0
> >> compressibility     =  4.5e-5
> >> ref_p               =  1.0
> >>
> >> What should I change in the .mpd file?
> >> Thank you very much.
> >> Lucia
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>