[gmx-users] Dipole moment

[Rajiv Gandhi]

Dear Gromacs,

I am trying to install gromacs with mpi enabled in my cluster and i end
up with following error:

libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error

I can able to install gromacs in single precision without having trouble.
However, when i use mpi enabled by using lam-7.4.1 it gives above mentioned
error, I have tried openmpi also but its not even compile it and ends up
with error like

configure: error: cannot compute sizeof (off_t)

I have used the command line ./configure --program-suffix=_mpi --enable-mpi
--enable-shared


I do not know how to solve this problem. Any suggestion would be
much appreciated.


Regards

Rajiv


On Fri, Oct 19, 2012 at 4:17 PM, Javier Cerezo <jcb1 at um.es> wrote:

> When calculated during the md run, the corresponding options in g_energy
> for the dipole moment are MU-X, MU-Y and MU-Z.
>
> However, taking into account the previous mail by David van der Spoel,
> it's possible that the dipole moment could not be calculated in your
> system. Options in g_energy vary depending on the actual computation.
>
> If you want to calculate the dipole moment by your own, I think it's
> easier to use the xtc file exported every 3fs (it'll be considerably
> heavier than the edr file, however) and writing an specific code for your
> purposes. In order to read the trajectories, you can use the xtc library (
> http://www.gromacs.org/**Developer_Zone/Programming_**Guide/XTC_Library<http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library>).
> Anyway, if the code didn't compute it, there should be a reason.
>
> Javier
>
>
> El 19/10/12 04:42, Nilesh Dhumal escribió:
>
>  Is it possible to calcualte the dipole moment at 3fs by modifing the
>> source code?
>>
>> Nilesh
>>
>>
>>  How can I save the total dipole moment extacted by .edr file?
>>>
>>> I could not find the option in g_energy.
>>>
>>> Nilesh
>>>
>>>
>>>  Justin is right. I've slipped a bit, that was not the way to set
>>>> nstenergy. But still, you can save the dipole directly in the edr file.
>>>> Not from your existing trajectory, but in a new run. Say your dt=1fs,
>>>> then you should set nstenergy=3 to get your dipole moment every 3fs
>>>> which you can retrieve with g_energy.
>>>>
>>>> Javier
>>>>
>>>>
>>>> El 18/10/12 20:43, Nilesh Dhumal escribió:
>>>>
>>>>> In short, I can not save dipole moment directly. I can calculate dipole
>>>>> moment only using .trr file.
>>>>>
>>>>> Nilesh
>>>>>
>>>>>> On 10/18/12 1:45 PM, Javier Cerezo wrote:
>>>>>>
>>>>>>> Hi
>>>>>>>
>>>>>>> The dipole is stored in the edr file, which output frequency is
>>>>>>> controlled by
>>>>>>> "nstenergy" option in the mdp parameter file. Set it appropriately
>>>>>>> during your
>>>>>>> run (nstenergy=0.003) but keep in mind that it should be a multiple
>>>>>>> of
>>>>>>> the time
>>>>>>> step.
>>>>>>>
>>>>>>>  nstenergy cannot be set this way; it is an integer indicating the
>>>>>> interval
>>>>>> (in
>>>>>> number of steps) for writing energy values.  If the values have been
>>>>>> saved
>>>>>> every
>>>>>> 2 ps, there is no way to retrieve them every 3 fs; if more frequent
>>>>>> information
>>>>>> is needed, it needs to be saved more frequently.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>  El 18/10/12 18:09, Nilesh Dhumal escribió:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I am calculating the dipole moment auto-correlation function for my
>>>>>>>> system
>>>>>>>> which have 128 cation and 128 anion.
>>>>>>>>
>>>>>>>> I am saving the trajectory at each 2 ps and using this trajectory
>>>>>>>> for
>>>>>>>> further analysis.
>>>>>>>>
>>>>>>>> Can I save the dipole moment and three vectors at each 3 fs?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Nilesh
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>  --
>>>>>> ==============================**==========
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Research Scientist
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>>
>>>>>> ==============================**==========
>>>>>> --
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>>>>>>
>>>>>>
>>>>>>  --
>>>> Javier CEREZO BASTIDA
>>>> Ph.D. Student
>>>> Physical Chemistry
>>>> Universidad de Murcia
>>>> 30100, Murcia (SPAIN)
>>>> T: (0034)868887434
>>>>
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>>
> --
> Javier CEREZO BASTIDA
> PhD Student
>
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
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