I tried the following code in cpptraj, but it seems to not be doing
anything. Any idea of what could I be doing incorrectly?
parm dna-nowater.prmtop
trajin md-nowater.mdcrd
rms first :1-24&!.H=
average crdset
createcrd trajj1
run
reference crdset
crdaction trajj1 rms ref crdset :1-24&!.H=
createcrd CRD1
trajout 1.mdcrd mdcrd
run
On Fri, Dec 30, 2016 at 9:23 PM, The Cromicus Productions <
thecromicusproductions.gmail.com> wrote:
> Thanks! I'm currently playing with that
>
> On Fri, Dec 30, 2016 at 4:21 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> May be perform best fit RMSD to reference (starting) structure by cpptraj?
>>
>> Hai
>>
>> On Fri, Dec 30, 2016 at 2:54 PM, The Cromicus Productions <
>> thecromicusproductions.gmail.com> wrote:
>>
>> > Hi everyone,
>> >
>> > I would like to know if there is an easy way to remove the motion
>> > of the center of mass of a molecule after I have obtained the
>> > trajectory (.mdcrd and .mdvel) files.
>> >
>> > Thanks a lot,
>> >
>> > Sebastian
>> > _______________________________________________
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>> >
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>
>
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Received on Sat Dec 31 2016 - 00:00:03 PST
