Hi,
Can anybody tell me why these two tools give different temperature values
based on same trajectory and input files?
1- g_energy_d -f md_shor.edr -s topol_shor.tpr -o T.xvg
0.00 508.066786
1.00 496.066137
2.00 501.665712
3.00 498.809896
4.00 499.
On 7/10/14, 12:49 PM, Rasoul Nasiri wrote:
Hi,
Can anybody tell me why these two tools give different temperature values
based on same trajectory and input files?
1- g_energy_d -f md_shor.edr -s topol_shor.tpr -o T.xvg
0.00 508.066786
1.00 496.066137
2.00 501.
Is there any other (not g_energy) tools in GROMACS to estimate T properly?
Rasoul
On Thu, Jul 10, 2014 at 5:51 PM, Justin Lemkul wrote:
>
>
> On 7/10/14, 12:49 PM, Rasoul Nasiri wrote:
>
>> Hi,
>>
>> Can anybody tell me why these two tools give different temperature values
>> based on same tra
On 7/10/14, 12:58 PM, Rasoul Nasiri wrote:
Is there any other (not g_energy) tools in GROMACS to estimate T properly?
Why is there a need for that when it's one of the normal functions of g_energy?
The values produced from the .edr file are the most accurate that you can get
because it st
Because
1- Estimation of T for different sub-systems say phases of gas, interface
and liquid.
Can be obtained with g_energy?
2- My trajectory is not constrain one as it has been recorded using
reactive FF.
I need to estimate T with converted trajectory (reaxff>gro).
Rasoul
On Thu, Jul
On 7/10/14, 7:09 PM, Rasoul Nasiri wrote:
Because
1- Estimation of T for different sub-systems say phases of gas, interface
and liquid.
Can be obtained with g_energy?
No, not unless they are assigned as separate tc-grps in the .mdp file, but then
(1) you shouldn't be designing something af
On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul wrote:
>
>
> On 7/10/14, 7:09 PM, Rasoul Nasiri wrote:
>
>> Because
>>
>> 1- Estimation of T for different sub-systems say phases of gas, interface
>> and liquid.
>> Can be obtained with g_energy?
>>
>>
> No, not unless they are assigned as separate
On 7/10/14, 9:30 PM, Rasoul Nasiri wrote:
On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul wrote:
On 7/10/14, 7:09 PM, Rasoul Nasiri wrote:
Because
1- Estimation of T for different sub-systems say phases of gas, interface
and liquid.
Can be obtained with g_energy?
No, not unless they
On Fri, Jul 11, 2014 at 10:27 PM, Justin Lemkul wrote:
>
>
> On 7/10/14, 9:30 PM, Rasoul Nasiri wrote:
>
>> On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul wrote:
>>
>>
>>>
>>> On 7/10/14, 7:09 PM, Rasoul Nasiri wrote:
>>>
>>> Because
1- Estimation of T for different sub-systems say p
Please just tell me how values of obtained T by g_traj can be corrected
> when I use trajectory and tpr files of constrain MD simulations (OPLS) as
> an input?
>
T(corrected) = T(g_traj)*natoms/(natoms-nconstraints)
Cheers,
Tsjerk
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On Sat, Jul 12, 2014 at 8:03 AM, Tsjerk Wassenaar wrote:
> Please just tell me how values of obtained T by g_traj can be corrected
> > when I use trajectory and tpr files of constrain MD simulations (OPLS) as
> > an input?
> >
>
>
> T(corrected) = T(g_traj)*natoms/(natoms-nconstraints)
>
>
T(g_tr
Note that two constrained atoms correspond to one constraint.
Cheers,
T.
On Jul 12, 2014 12:01 PM, "Rasoul Nasiri" wrote:
> On Sat, Jul 12, 2014 at 8:03 AM, Tsjerk Wassenaar
> wrote:
>
> > Please just tell me how values of obtained T by g_traj can be corrected
> > > when I use trajectory and t
On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar
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 ce
On 7/12/14, 7:25 AM, Rasoul Nasiri wrote:
On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar
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
On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote:
>
>
> On 7/12/14, 7:25 AM, Rasoul Nasiri wrote:
>
>> On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar
>> wrote:
>>
>> Note that two constrained atoms correspond to one constraint.
>>>
>>>
>>>
>>
>> C12H26
>>
>> 26 constrained atoms due to
On 7/13/14, 7:11 PM, Rasoul Nasiri wrote:
On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote:
On 7/12/14, 7:25 AM, Rasoul Nasiri wrote:
On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar
wrote:
Note that two constrained atoms correspond to one constraint.
C12H26
26 constrain
On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul wrote:
>
>
> On 7/13/14, 7:11 PM, Rasoul Nasiri wrote:
>
>> On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote:
>>
>>
>>>
>>> On 7/12/14, 7:25 AM, Rasoul Nasiri wrote:
>>>
>>> On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar
wrote:
>
On 7/13/14, 8:41 PM, Rasoul Nasiri wrote:
On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul wrote:
On 7/13/14, 7:11 PM, Rasoul Nasiri wrote:
On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote:
On 7/12/14, 7:25 AM, Rasoul Nasiri wrote:
On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wasse
On Mon, Jul 14, 2014 at 12:51 PM, Justin Lemkul wrote:
>
>
> On 7/13/14, 8:41 PM, Rasoul Nasiri wrote:
>
>> On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul wrote:
>>
>>
>>>
>>> On 7/13/14, 7:11 PM, Rasoul Nasiri wrote:
>>>
>>> On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul wrote:
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