[gmx-users] Dr.Lemkul's Umbrella Sampling Tutorial - grompp note on leap frog/Nose-Hoover

Agnivo Gosai agnivogromacs14 at gmail.com
Tue Nov 4 20:49:45 CET 2014

Dear Users

I read on the web and understood that the warning note can be avoided by
selecting integrator = md-vv instead of integrator = md. This will increase
computation time.
Also if I go ahead with Nose-Hoover thermostat and integrator = md it may
not cause any appreciable problem for my protein complex as discussed in
similar posts in the gmx forums.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

On Mon, Nov 3, 2014 at 6:37 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>

> Dear Users
> I am following the Umbrella Sampling tutorial by Dr. Lemkul. I am using
> GROMACS version 4.5.6.
> In step 6 of the tutorial where the umbrella sampling simulations are done
> for each of the extracted configurations based on COM distance sampling
> from 0.5 - 5.0 nm along z axis , I have 27 sets.
> For each set I need to do a short NPT equilibration and an Umbrella run.
> While running "grompp" for the 1st configuration before the NPT
> equilibration the terminal showed the following message :
> NOTE 1 [file md_umbrella.mdp]:
>   leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to
> 1
> My question is how will this affect my simulations ?
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.

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