[gmx-users] Hello

[Justin Lemkul]

On 11/12/14 8:56 AM, Anik Sen wrote:
> Dear Sir/madam,
>                                 Below is a .mdp file for running the equilibration of my protein sample in water. I am using temperature coupling as well as pressure coupling. This indicates of doing a NPT ensemble, right??
>

Yes.

> For NVT ensemble, what should i do, just do a temperature coupling?
>

Yes.

> Please let me know,,,,
>

Consult some basic tutorials (there are many available) if fundamental issues 
are not clear.  Also note that tau-t = 0.0 for protein will not preserve the 
temperature of the protein atoms.

-Justin

> Anik Sen
>
>   title             =  trp_drg
> warning             =  10
> cpp                 =  /usr/bin/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.001 ; ps !
> nsteps              =  250000 ; total 500.0 ps.
> nstcomm             =  100
> nstxout             =  250 ; ouput coordinates every 0.5 ps
> nstvout             =  1000 ; output velocities every 2.0 ps
> nstfout             =  0
> nstlog              =  100
> nstenergy           =  100
> nstlist             =  100
> ns_type             =  grid
> rlist               =  1.0
> coulombtype         =  PME
> rcoulomb            =  1.0
> vdwtype             =  cut-off
> rvdw                =  1.0
> fourierspacing      =  0.12
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  6
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
> ; V-rescale temparature coupling is on
> Tcoupl              =  V-rescale
> tau_t               =  1.0    0.0
> tc_grps             =  SOL   protein
> ref_t               =  300    300
> ; Pressure coupling is on
> pcoupl              =  berendsen ; Use Parrinello-Rahman for research work
> pcoupltype          =  isotropic ; Use semiisotropic when working with membranes
> tau_p               =  2.0
> compressibility     =  4.5e-5
> ref_p               =  1.0
> refcoord-scaling    =  all
> ; Generate velocites is on at 300 K.
> gen_vel             = yes
> gen_temp            = 300.0
> gen_seed            = 173529
>
>
>
> *** STK-14 Uppsala *** https://sites.google.com/site/stkmuu14/
> Dr. Anik Sen,
> Post Doctoral Fellow,
> Ångströmlaboratoriet- Uppsala Universitet
> Box 538
> SE-751 21 Uppsala
> Sweden
> Phone no:- +46-722781705
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================