[gmx-users] Set up anti parallel membrane system for CompEL simulation

[Jochen Hub]

Am 04.05.20 um 23:21 schrieb Jochen Hub:
> 
> 
> Am 04.05.20 um 21:33 schrieb Zheng Ruan:
>> Hi,
>>
>> I'm trying to setup an antiparallel membrane system for CompEL 
>> simulation.
>> It is relatively straightforward to convert an existing single membrane
>> system to a parallel system by using
>>
>> # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro
>>
>> However, is there an easy way to invert one of the membrane protein
>> configurations along with the membrane, water and ions?
> 
> You could try:
> 
> gmx editconf -rotate 90 0 0

Sorry, I meant of course editconf -rotate 180 0 0

You probably have to combine this with an editconf -translate, together 
with a manual extension of the box by 1-2 Angstroem to avoid overlapping 
water molecules at the box edge.

Jochen

> 
> Cheers, Jochen
> 
>>
>> Thanks,
>> Zheng
>>
> 

-- 
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Prof. Dr. Jochen Hub
Theoretical Biophysics Group
Department of Physics, Saarland University
Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany
Phone: +49 (0)681 302-2740
https://biophys.uni-saarland.de/
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