[gmx-users] NPT equilibration

[Deep Bhattacharya]

Yes the average after NPT equilibration

Sincerely,
Deep

On Mon, Jul 11, 2016 at 2:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/11/16 3:48 PM, Deep Bhattacharya wrote:
>
>> Thank you Mark.
>> So this pressure value that I am getting is normal correct?
>>
>>
> When you say "pressure after NPT," do you mean that is the average over
> NPT or is that the instantaneous value of the final frame?  If the former,
> I would expect you could achieve better but the fluctuations are going to
> be large.  If the latter, it means nothing.
>
> -Justin
>
>
> Sincerely,
>> Deep
>>
>> On Mon, Jul 11, 2016 at 2:42 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> See http://www.gromacs.org/Documentation/Terminology/Pressure
>>>
>>> Mark
>>>
>>> On Mon, Jul 11, 2016 at 9:40 PM Deep Bhattacharya <
>>> hypergenetics at gmail.com
>>>
>>>>
>>>> wrote:
>>>
>>> Hello,
>>>>
>>>> I am have done NVT and NPT equilibration on my complex which is
>>>> protein-carbohydrate solvent complex. I am getting -117.4 bar as my
>>>> pressure after NPT.
>>>> What could be a possible explanation to this?
>>>> I have attached the NPT.mdp below
>>>>
>>>> title = PP
>>>> define       =  -DPOSRES -DPOSRES_LIGAND; position restrain the protein
>>>> ; Run parameters
>>>> integrator = md ; leap-frog integrator
>>>> nsteps = 2500000 ; 0.001 * 2500000 = 2500 ps
>>>> dt    = 0.001 ; 1 fs
>>>> ; Output control
>>>> nstxout = 0 ; save coordinates every 1.0 ps
>>>> nstvout = 0 ; save velocities every 1.0 ps
>>>> nstenergy = 0 ; save energies every 1.0 ps
>>>> nstlog = 1
>>>> nstxtcout   = 0
>>>> energygrps  = Protein LIG
>>>> ; 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         = 1        ;
>>>> rcoulomb        = 0.8
>>>> rvdw            = 0.8
>>>> coulombtype     = Cut-off       ; Particle Mesh Ewald for long-
>>>> vdwtype        = cut-off
>>>> rlistlong      = 1.4
>>>> epsilon-rf     = 61
>>>> rlist          = 0.75
>>>> ; Temperature coupling is on
>>>> tcoupl = nose-hoover            ; modified Berendsen thermostat
>>>> tc-grps       =Protein_LIG Water_and_ions   ; two coupling groups - more
>>>> accurate
>>>> tau_t = 2.0  2.0        ; time constant, in ps
>>>> ref_t = 300  300        ; reference temperature, one for each group, in
>>>> K
>>>> ; Pressure coupling is on
>>>> pcoupl        = Parrinello-Rahman            ; Pressure coupling on in
>>>>
>>> NPT
>>>
>>>> pcoupltype        = isotropic            ; uniform scaling of box
>>>> vectors
>>>> tau_p        = 6.0            ; 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
>>>>
>>>> Please help.
>>>> --
>>>>
>>>> *Deep S Bhattacharya*
>>>>
>>>> *Graduate Research Assistant*
>>>>
>>>> Mohs Biomedical Imaging & Nanotechnology Group
>>>>
>>>> Pharmaceutical Sciences
>>>>
>>>> *University of Nebraska Medical Center*
>>>>
>>>> 4018 Eppley Science Hall  |  Omaha, NE 68198-6805
>>>>
>>>> office 402.559.4349  | cell 402.906.1640
>>>>
>>>> deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
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>>
>>
>>
> --
> ==================================================
>
> 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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-- 
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616