[gmx-users] inconsistency in obtained temperature values by traj and g_energy tools

[Justin Lemkul]

On 7/12/14, 7:25 AM, Rasoul Nasiri wrote:
> On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
>> Note that two constrained atoms correspond to one constraint.
>>
>>
>
>
> C12H26
>
> 26 constrained atoms due to hydrogens which have been connected to carbon
> atoms.
>
> Number of molecules 2550 therefore  66300 will be total constrained atoms
> in cell.
>

Note that grompp makes your life easy by printing out the corrected number of 
degrees of freedom.  It should be 3N - 0.5*N_constraints.

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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