[gmx-users] Help with gmx make_ndx

Quyen V. Vu vuqv.phys at gmail.com
Wed Aug 24 06:28:40 CEST 2016


Mark Abraham:
> If you want to engage in discussion, please don't subscribe to the digest
> and then reply to its emails. That makes it painful for everyone to follow
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I'm very sorry for my stupid ( I am new to mailing list so not familiar
with reply)
>> I think if I type 8|9 then my index.ndx should not appear [systems] group
>>(
>> it too large for my system)

>Yes, it should, because you asked it to make a subset of a file that had
>the full system...

So, could you tell me how to get only index of LA and CL group when
make_ndx prompt like this?
Select group for output
Group     0 (         System) has 943920 elements
Group     1 (            DNA) has  3198 elements
Group     2 (             LA) has    76 elements
Group     3 (             CL) has   130 elements
Group     4 (          Water) has 940516 elements
Group     5 (            SOL) has 940516 elements
Group     6 (      non-Water) has  3404 elements
Group     7 (            Ion) has   206 elements
Group     8 (             LA) has    76 elements
Group     9 (             CL) has   130 elements
Group    10 ( Water_and_ions) has 940722 elements

what should I type ?


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