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

Luis Felipe Pineda de Castro luis.pinedadecastro at lnu.se
Fri Apr 5 22:02:00 CEST 2013

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" 



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
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)

Abhishek Acharya
Structural and Computational Biology Lab
Indian Institute of Technology Kanpur

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