[gmx-users] Do i need to put POSITION RESTRAINT DURING EQUILIBRATION STAGE ( NVT&NPT ) if i am preparing an amorphous sample?

Krzysztof Makuch krzysztof.makuch at gmail.com
Sat Feb 10 00:30:31 CET 2018

That's always your call. You perform equilibration to swap between MM
(energy minimization) and MD (kinetic energy). In the other word you slowly
start MD and prevent unwanted and unrealistic rearrangement in your system.
If initial positions are important - you restrain the interesting
molecules. If you equilibrate for example lipid bilayer - there is no
reason to do that. Often you can also totally skip equilibration and just
cut off a few initial ns. Sometimes you make nvt, npt and still cut off
beginning and sometimes you perform MD to find optimal system, in which
case the whole simulation is in fact equilibration.
You know your system, you have to consider if restraining movement is what
you need.

2018-02-09 13:28 GMT+01:00 sanjeet kumar singh ch16d012 <
ch16d012 at smail.iitm.ac.in>:

> Hi list,
> I am preparing an amorphous sample using GROMACS but i am in doubt that
> during the equilibration stage ( NVT & NPT ) do i need to put position
> restraint on my polymer as there are no solvent in my system and if i have
> to use position restraint then why i should do that?
> SK
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