[gmx-users] gmx grompp

[Dallas Warren]

That depends entirely on what is of interest from the simulation, and only
you know those details.  For most situations, as you noted, it isn't a
concern, but you need to ensure that is actually the case.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 16 Apr 2019 at 12:08, Amin Rouy <aminrou1986 at gmail.com> wrote:

> Thank you Justin. Yes, you are right as i noticed when tested the
> simulations with -t and without. However, i think it is not dangreous
> physically and the final results remain the same. Am i right?
>
> On Tue, Apr 16, 2019, 01:05 Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 4/15/19 8:36 AM, Amin Rouy wrote:
> > > Hi,
> > >
> > > Providing -t flag in grompp (gmx grompp -t nvt.cpt) is optional
> according
> > > to documentation. How does it influence on results?
> >
> > Checkpoint files are necessary for exact continuations.
> >
> > > I'm asking because I have finished my simulation and only gave -c
> > nvt.gro,
> > > not -t npt.cpt. Are my results correct?
> >
> > You're relying on limited precision for coordinates and velocities, and
> > you will lose other state variables. Thus, the continuation is not exact.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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