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

[Agnivo Gosai]

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.

[Justin Lemkul]

Post by Agnivo Gosai
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
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
My question is how will this affect my simulations ?

It's an innocuous message. There are inherent limitations in compatibility of
various algorithms and options. Notes are simply FYI. Warnings and errors
indicate problems.

-Justin
--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

***@outerbanks.umaryland.edu | [phone]
http://mackerell.umaryland.edu/~jalemkul

==================================================

[Agnivo Gosai]

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.

Post by Agnivo Gosai
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
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.