[gmx-users] genion doesn't work in 4.6.1?

[Abhishek Acharya]

> Again and again posting from Abhishek Acharya or Shima, or Rama David or
> somehow else ... pls read my posting before, it could be useful for you,
> Indian fellows ... maybe it's possible to get some kind of agreement
> though brahmin.net or so ..
>
> Best regards of somebody experienced with Indian "science"
>
> Best,
>
> Felipe

Dear Luis
I hope you do realize that this is a open for all forum to discuss and
sort out problems. And also that posting such prejudiced comments are not
in the right spirit for this or any other forum related to science. But
since you have posted I would take the opportunity for once to point out
that if there were any shortage of supervision, there would be about a
1000 queries alone from Indians each day. So the take home message is that
only people who don't have anyone in the vicinity to solve their problems
and are stuck, post questions on this forum, and this is not in any way a
function of the geographical region or race a person belongs. Can happen
to anyone.
I hope in the future you don't bring your personal prejudices, whatever
may be your experience with Indian science, into this forum.

With Regards
Abhishek Acharya
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of Abhishek Acharya [aacharya at iitk.ac.in]
> Sent: Friday, April 05, 2013 9:35 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] genion doesn't work in 4.6.1?
>
>> On 04/05/2013 09:09 PM, Warren Gallin wrote:
>>> Don't you have to give tyne name of the positive and negative ions that
>>> will be added by genion?  Otherwise, how would it know?
>>>
>>> Warren Gallin
>>
>> No, it doesn't work either:
>>
>> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
>> -norandom -pname NA -nname CL
>>
>> or
>>
>> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
>> -norandom -pname NA -pq 11
>>
>> Reading file ions.tpr, VERSION 4.6.1 (single precision)
>> Using a coulomb cut-off of 1.2 nm
>> No ions to add and no potential to calculate.
>>
> You are using the wrong combinations of flags:
>  Either of the following should do the job:
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -pname NA -np 11
> -pq 1
> or
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -conc 0.15 -neutral
> (incase you want a NaCl conc of 0.15 M. Only in this case, genion will
> automatically add NA and CL ions to neutralize the charge and sufficiently
> reach the given conc., in this case 0.15 M)
>
> Cheers.
> Abhishek Acharya
> Structural and Computational Biology Lab
> Indian Institute of Technology Kanpur
>
>
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