just want to point out that user can also install the most updated cpptraj
version from github
git clone
https://github.com/Amber-MD/cpptraj
Hai
On Sun, Aug 9, 2015 at 5:15 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Yes, just download AmberTools 15 for free: http://ambermd.org/#AmberTools
>
> Hai
>
>
> On Sun, Aug 9, 2015 at 4:50 PM, Amber mail <amber.auc14.gmail.com> wrote:
>
>> Dear dac,
>>
>> Thanks a lot for your help!
>>
>> Is it possible to upgrade ambertools 12 to ambertools 15 freely, or should
>> I get the full Amber 15 package ?!
>>
>> Best Regards,
>> Alaa
>> On Aug 9, 2015 3:03 PM, "David A Case" <david.case.rutgers.edu> wrote:
>>
>> > On Sun, Aug 09, 2015, Amber mail wrote:
>> >
>> > > > rms reference mass out 02_03.rms time 10 :44-61
>> > > >
>> > > 1- Does the " time 10 " indicate the time of each frame in ps ?
>> >
>> > It tells cpptraj the time between snapshots, in whatever units you wish.
>> > (ps or ns are common units). This is only used to replace the frame
>> number
>> > with the elapsed time in writing some output files.
>> > >
>> > > This how I calculated the value of 10
>> > >
>> > > No. of frames = nstlim/ ntpr =5000000/5000=1000 frame
>> >
>> > You should use ntwx, not ntpr, here. In your example, they are both the
>> > same.
>> >
>> > >
>> > > Simulation time =nstlim*dt = 5000000*0.002=10000 ps
>> > >
>> > > Time of each frame = simulation time/no.frames= 10 ps
>> >
>> > Works. But simpler is just ntwx*dt.
>> > >
>> > > 2- Does " :44-61 " mean to specify residues from 44-61 only?
>> >
>> > Yes.
>> >
>> > >
>> > > Should I also add the command " strip: WAT " to exclude all water
>> > molecules
>> > > from RMSD ?
>> >
>> > You don't need this, unless some of the residues 44-61 are in fact water
>> > molecules. (But in that case, you should just change ":44-61" to what
>> you
>> > really want.)
>> >
>> > > So does this graph represent the time of MD simulation in (ps) on
>> x-axis
>> > > and the RMSD in (Angstroms) on y-axis ?
>> >
>> > Yes.
>> >
>> > >
>> > > I just want to double check my work because I am not sure that I well
>> > > understand the part concerned with cpptraj in AmberTools12 Manual
>> >
>> > I strongly urge you to upgrade to AmberTools15. cpptraj is being
>> developed
>> > now at a very rapid pace. Simple tools like "rms" are probably fine in
>> the
>> > older version, but many bugs have been fixed and new feature added.
>> Even
>> > the manual is better (although still far from perfect.)
>> >
>> > ....good luck....dac
>> >
>> >
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
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Received on Sun Aug 09 2015 - 16:30:03 PDT
