From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Sun Jan 31 2010 - 23:25:36 CST
the most convenient way to work with dcd files is using "catdcd" utility.
just google it, it can do many helpful things. for example,
https://bmiwiki.cchmc.org/index.php/Catdcd
On Sun, Jan 31, 2010 at 11:58 PM, ipsita basu <ibasu788_at_gmail.com> wrote:
> Dear all,
> I have run a very short simulation of 500 ps. In the input dcd
> freq was 2500 and the total step is 250000 and time step 2 fs ( tot 500 ps
> ). Now I want to convert the dcd to crd for the final step to see the final
> situation. That's why the output.dcd was read in charmm and the command was
> :
> coor dyna firstu 51 nunit 1 begin 250000 stop 250000 .
> But the log file gives error like :
> READING TRAJECTORY FROM UNIT 51
> NUMBER OF COORDINATE SETS IN FILE: 100
> NUMBER OF PREVIOUS DYNAMICS STEPS: 2500
> FREQUENCY FOR SAVING COORDINATES: 2500
> NUMBER OF STEPS FOR CREATION RUN: 250000
>
> ***** ERROR ***** NO. OF ATOMS DO NOT MATCH 29566 27334
> *** LEVEL -4 WARNING *** BOMLEV IS 0
> BOMLEV HAS BEEN SATISFIED. TERMINATING.
> But if I change the begin step to 2500 and stop also 2500, then there is no
> problem.
> So what should I do to solve the problem? Please help me.
>
>
> Thanking You
>
> Ipsita Basu
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009
-- Thanks, Roman Petrenko
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