[gmx-users] Dipole moment

Fri Oct 19 11:09:01 CEST 2012

Dear Rajiv,

Please start a different thread, if you want to get help. I suppose
you need to be informative regarding your error(s).

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA

On Fri, Oct 19, 2012 at 2:07 PM, Rajiv Gandhi <grajiv03 at gmail.com> wrote:
> 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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