[gmx-users] Re: 1/viscosity from g_energy

Vitaly Chaban vvchaban at gmail.com
Sat Apr 16 23:24:04 CEST 2011

> Dear all,
> I figured out the problem. Error was in my mdp file options. I did not
> specify the acc-groups correctly. I can get 1/viscosity using g_energy.
> However, once the acc-groups are specified, now the NEW issue is not being
> able to run my job correctly.
> I get the following errors:
> Step 376, time 7.52 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.006964, max 0.163855 (between atoms 861 and 859)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length

1. To get viscosity from non-eq. MD, you should specify ONLY
"cos_acceleration" in the MDP and then use g_energy utility.

2, To get viscosity from eq. MD, use "g_energy -vis", while saving the
energy terms every 10-30 fs.

Your problems with lincs are probably connected with a high value for
acceleration. The first step is to decrease it.

Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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