[gmx-users] Queries related to parameterization

[Smruti Sanjita Mishra]

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??

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??

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??

waiting for your response :)
Kind Regards,
Smruti Mishra
Bioinformatics Intern - IIIT-H
Dr. Deva Lab (Computational Biology - CCNSB)
Hyderabad - 500032