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

Rasoul Nasiri nasiri1355 at gmail.com
Mon Jul 14 02:41:05 CEST 2014

```On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/13/14, 7:11 PM, Rasoul Nasiri wrote:
>
>> On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> 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.
>>>
>>>
>>>
>>>  Based on grompp_d:
>>
>> Number of degrees of freedom in T-Coupling group System is 196338.00
>>
>> 3N-0.5*N_constrants = 196338
>>
>> N= 96900
>> ===.> N_constraints =188706
>>
>> T(corrected) = T(g_traj)*N_atoms/(N_atoms-N_constraints)
>>
>> T(g_traj) = 269 K
>> N_atoms = 96900
>>
>> ==> T(corrected) = -262 which is unphysical value.
>>
>> any other suggestions/solutions?
>>
>> Note that the desired temperature is 400 K.
>>
>>
> You're doing the calculation wrong.
>
> Number of degrees of freedom that g_traj assumes: 96900 * 3 = 290700
>

I think translational modes should be reduced, having said this for N total
atoms with fixed mumentum into the cell (290700-3) must be more accurate.

> Number of actual degrees of freedom from grompp: 196338
>
>

> Temperature conversion factor = 290700/196388 = 1.481
>

It makes sense.

>
> Actual T = 269 * 1.481
> Actual T = 398.3 K
>
>
Thanks.

> -Justin
>
>
Rasoul

>
> --
> ==================================================
>
> 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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