[gmx-users] Implicit solvent - Gromacs 4.5.4

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 28 15:50:19 CET 2012

Vedat Durmaz wrote:
>   actually, as far as i know, the -DFLEXIBLE argument has no effect on 
> simulations without explicit water ?!

The #ifdef FLEXIBLE block does only affect explicit water, unless the topology 
is somehow modified to use this type of term (probably not).  It shouldn't be 
used for MD anyway, as all water models were parameterized to be rigid.

> i just copied the "define" line from my explicit simulation systems .. 
> so, the only define value, that has a meaning is -DPOSRESHELIX.
> i didn't use constraints for the first time in my life since implicit 
> solvent simulations incorporate a much smaller number of atoms and are 
> therefore not that expensive computationally. i always use this setting 
> for my explicit simulations only in order to increase the step size to 
> 2fs with a clear conscience ...

One should also consider the representation of the physical model.  It can be 
argued that rigid bonds are a more realistic representation of ground state 
bonds, in addition to making the simulations more efficient.



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


More information about the gromacs.org_gmx-users mailing list