Re: [gmx-users] adding polyatomic species in water

[Kester Wong]

Check whether the configuration of the atom with highest force is configured reasonably.

If you are only getting a few minimisation steps before crashing, then perhaps minimising your cell using a double precision GROMACS would help?

Cheers,

Kester

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보낸사람 : #SUKRITI GUPTA# <sukriti...@e.ntu.edu.sg>
받는사람 : "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
받은날짜 : 2015년 2월 4일(수) 19:10:26
제목 : [gmx-users] adding polyatomic species in water

Dear Gromacs Users,


I am trying to simulate a cell containing different polyatomic species like sulphate, glucose, acetic acid etc. in water. I start my simulation by taking pdb file containing 1 sulphate ion and then add remaining sulphate ions and other species using -cs and -ci from genbox. I use genbox command multiple time till all the species are added and system is solvated in water. But when I perform energy minimisation, the initial system starts with a very high energy i.e. around 10^6 range and the either it doesn't get converged or i get msg Segmentation fault (core dumped).


I also tried using genconf but still i was getting the same problem.


Can anyone please let me know what is wrong with my system and how can i correctly add all the species in my system.


Regards

Sukriti


[https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif]

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg


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