Hi Dan,
Thanks! Your suggestion to use two consecutive closest commands worked perfectly for my purpose.
Best,
Matthew
> On Apr 9, 2022, at 10:33 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hi,
>
> On Sat, Apr 9, 2022 at 5:59 AM Matthew Guberman-Pfeffer
> <matthew.guberman-pfeffer.uconn.edu> wrote:
>> I want to write a trajectory where I only retain the WAT and Na+ residues within the first salvation shell.
>
> As you've discovered you cannot do this with a single 'closest'
> command, the reason being that if you have two different types of
> "solvent" molecule and a single target number, the number of atoms
> could change from frame to frame (e.g. 3000 WAT plus 412 Na+ is a
> different number of atoms than 3200 WAT and 212 Na+, etc).
>
> You can do something like what you want with separate 'closest'
> commands. You can run one 'watershell' command to see how many waters
> are in the first solvation shell, then a second 'watershell' command
> to do the same for Na+. Then say you want to keep the 3400 closest WAT
> and 12 closest Na+, you can use something like:
>
> # Closest 3400 waters to molecule 1
> closest 3400 ^1
> # Closest 12 Na+ to molecule 1
> closest 12 ^1 solventmask :Na+ parmout closest.parm7
> trajout closest.nc
>
> Hope this helps,
>
> -Dan
>
>> I’ve used the watershell command in CPPTRAJ to figure out that there are 3412 :WAT or :Na+ molecules within 3.4 Å on average.
>> I then tried to use the solvent command and the closest command, but it complained that the solvent (defined as :WAT,Na+) was not all of the same size.
>> I’m now thinking of directly using the strip command, but my understanding is that it will not update a distance-based selection for the solvent on each new frame. Is that right?
>> How can I write a trajectory that retains only the waters and Na+ ions within the first salvation shell?
>>
>> Best,
>> Matthew
>>
>>
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Received on Sat Apr 09 2022 - 18:30:02 PDT
