[gmx-users] NPT equilibration in KALP15-DPPC

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Aug 27 08:30:35 CEST 2012


After the NPT mdrun, I visulized the npt.gro. 
I need to know if this npt.gro is the final result of equilibration?
I see 2,3 water molecules between the lipid chains. Should I remove them? Can I remove them? Or it's not the step that I can make such a decision?

Thanks in advance.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, August 26, 2012 5:29 PM
Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC

On 8/26/12 8:54 AM, Shima Arasteh wrote:
> Hi,
> For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when
> I run the grompp command, I get 4 notes. Is it necessary to pay attention to
> the notes ? Are they notable?

Notes are generally notable, yes ;)  Never ignore anything grompp tells you, 
that's my rule of thumb.  Some messages are less critical than others.  The ones 
shown here are quite important.

These warnings cannot possibly be produced by the .mdp file in the tutorial, and 
they suggest that you are not doing NPT under any sort of stable conditions. 
You're using plain cutoffs, no constraints, and attempting to produce NVE, which 
will surely fail.


> NOTE 1 [file npt.mdp]: You are using a cut-off for VdW interactions with NVE,
> for good energy conservation use vdwtype = Shift (possibly with DispCorr)
> NOTE 2 [file npt.mdp]: You are using a cut-off for electrostatics with NVE,
> for good energy conservation use coulombtype = PME-Switch or
> Reaction-Field-zero
> Generated 837 of the 2346 non-bonded parameter combinations Excluding 3
> bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours
> molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'CL'
> NOTE 3 [file topol.top, line 929]: The bond in molecule-type Protein between
> atoms 4 N and 5 H has an estimated oscillational period of 1.0e-02 ps, which
> is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change
> the constraints mdp option.
> Number of degrees of freedom in T-Coupling group rest is 33897.00
> NOTE 4 [file npt.mdp]: You are using a plain Coulomb cut-off, which might
> produce artifacts. You might want to consider using PME electrostatics.
> Reading Coordinates, Velocities and Box size from old trajectory Will read
> whole trajectory Last frame         -1 time  100.000 Using frame at t = 100
> ps Starting time for run is 0 ps Largest charge group radii for Van der
> Waals: 0.239, 0.234 nm Largest charge group radii for Coulomb:       0.239,
> 0.234 nm This run will generate roughly 1 Mb of data
> There were 4 notes
> Thanks for your suggestions in advance.
> Sincerely, Shima


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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