[gmx-users] Queries related to parameterization

[Justin Lemkul]

On 12/9/19 12:05 AM, Smruti Sanjita Mishra wrote:
> Hello Sir/Ma'am
>
> Greetings!
>
> Apologies for the unprecedented message.
>
> I am smruti and being a beginner in gromacs and molecular dynamics field ,
> I have some doubts, that I want to clear.
>
> 1. My system is just protein , water and some ions. if I am using
> charmm27(charmm22 + cmap) and during the solvent model selection, I chose
> TIP3P.itp but it did not run, instead it showed error, that tip3p file has
> been removed from gromacs/share/top. is it ok to use spc216.gro in the
> place of tip3p as they all are three point models.?? and is charmm 27 and
> spc216 is the right combination for the system?? and if I want to use tip3p
> then how can i proceed with it??

The relocation of tip3p.itp to individual force field subdirectories is 
separate from the location of coordinate files. There has never been a 
tip3p.gro with GROMACS since any 3-point water model coordinates can be 
used for solvation. The one provided is spc216.gro but after a brief 
equilibration, these coordinates will respond to the properties of the 
TIP3P model.

> 2. In the energy minimization input file(.mdp) if i want to change the
> default integrator = steep into ABNR Algorithm then how can i change and
> what is the difference basically between two algorithms??

GROMACS does not support ABNR. That's an algorithm in CHARMM.

> 3. In nvt.mdp file, when I changed tcoupl = V-rescale ; modified Berendsen
> thermostat into Nose-Hoover it ran upto some steps and then suddenly showed
> segmentation error. is it due to the change of default method or any other
> reason? and if i want to continue with nose-hoover method then how should i
> proceed with it??

Nose-Hoover allows for wider fluctuations and is therefore unsuitable 
for an initial equilibration. Use V-rescale and switch after 
equilibration, if you want.

-Justin

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Justin A. Lemkul, Ph.D.
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