[gmx-users] parameters obtained after NPT

[Justin Lemkul]

On 3/25/15 11:17 AM, soumadwip ghosh wrote:
> Dear users,
>
>                   Firstly, I would like to thank Justin for helping me out
> in preparing  an initial system containing a single walled CNT and a ss-DNA
> for MD simulations. Previously I was using position restraint as well as
> freeze group for keeping my CNT fixed during equilibration steps and the
> system was blowing up and it was not minimized well. Now, I am  stuck with
> a new problem is that after the NPT run for about 5 ns, I am getting some
> weird pressure, density and volume from g_energy. The pressure is negative
> and the volume is nowhere close to the initial cell volume. Although the
> temperature is alright but the density is in hundreds while for TIP3P water
> models it should be around 1020 Kg M(-3). I want to see the volume (cell)
> reaching the desired values along with proper build-up of density and
> that's why I started NPT first instead of NVT. Is it happening because the
> npt.mdp file is wrong somewhere? Please help me out with this. I am using
> GROMACS 4.5.6 in conjugation with CHARMM 27 force field. The .mdp file is
> given below.
>

Use a modern software version and use correct settings.

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

Beyond that, the only thing that one can say is that your system is still 
exploding.  Based on your description, you should be able to visualize the 
trajectory and see some clearly incorrect behavior.

-Justin

>
> title           = ssdna          npt equilibration
> define          = -DPOSRES      ; position restrain the dna
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 4000000               ; 2 * 1000000 = 2000 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 500           ; save coordinates every 0.2 ps
> nstvout         = 500           ; save velocities every 0.2 ps
> nstenergy       = 500           ; save energies every 0.2 ps
> nstlog          = 1000          ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = yes           ; Restarting after NVT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 1             ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 1             ; short-range electrostatic cutoff (in nm)
> rvdw            = 1             ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = SYSTEM        ; three coupling groups - more accurate
> tau_t           = 0.1           ; time constant, in ps
> ref_t           = 300           ; reference temperature, one for each
> group, in K
> ; Pressure coupling is on
> pcoupl          = berendsen     ; Pressure coupling on in NPT
> pcoupltype      = isotropic     ; uniform scaling of box vectors
> tau_p           = 2.0           ; time constant, in ps
> ref_p           = 1.0           ; reference pressure, in bar
> compressibility = 4.5e-5        ; isothermal compressibility of water,
> bar^-1
> refcoord_scaling = com
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no            ; Velocity generation is off
>
> Thank you for your time in advance.
>
> Regards,
> Soumadwip Ghosh
> Research Fellow,
> IITB, mumbai
> India
>

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

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

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