Thank you, sir, for your reply. I am trying this using stfcdiffusion
command. Because I am trying to calculate the MSD of active site water
molecules (waters within 8 angstrom from Zn atom).
so parm *.prmtop
trajin *.nc
rms first #(as you recommended for internal coordinate changes)
stfcdiffusion mask :WAT.O out msd.dat time 5 mask2 :ZN6 lower 2.0 upper 8.0
nwout nw.dat avout avg.dat
go
Can I do that for active site MSD of water molecules?
Thanking you
On Wed, Dec 20, 2023 at 6:21 PM Steinbrecher, Thomas <
thomas.steinbrecher.roche.com> wrote:
> Are you interested in diffusive motion of your molecules or in internal
> coordinate changes? For the later you need to align the trajectory to
> remove translational and rotational motion, for the former you should not
> align it.
>
> For wrapping, based on the manual, the diffusion command in cpptraj does
> handle imaging automatically (see the noimage keyword of that command as
> well), so it can process both wrapped and unwrapped trajectories. The only
> thing that seems to not work is wrapped trajectories plus the noimage
> keyword.
>
> In any case, why not try both options and see if the results make sense?
>
> Kind Regards,
>
> Thomas
>
> On Wed, Dec 20, 2023 at 11:30 AM Dulal Mondal via AMBER <amber.ambermd.org>
> wrote:
>
>> **Warning** The sender address (Dulal Mondal via AMBER ) can not be
>> verified, sender email address could be spoofed. Please take care to
>> proceed.
>> Dear Experts,
>> I am trying to calculate mean square displacement using cpptraj. In the
>> input file ("mdin"), I set the iwrap=1 command. Is it mandatory to unwrap
>> the trajectory before analysis?
>> Again, is it mandatory to align the trajectory?
>>
>> Thanking You
>> --
>> *With regards,*
>> *Dulal Mondal,*
>> *Research Scholar,*
>> *Department of Chemistry,*
>> *IIT Kharagpur, Kharagpur 721302.*
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
> --
> *Dr. Thomas Steinbrecher*
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
>
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 20 2023 - 06:30:02 PST
