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

[Rasoul Nasiri]

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.


> -Justin
>
>
Rasoul

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