[gmx-users] NPT equilibration

[Justin Lemkul]

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
>>> --
>>> 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.
>>>
>> --
>> 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.
>>
>
>
>

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

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

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