Re: analysis of dcd

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Feb 01 2010 - 01:13:45 CST

Or, use VMD

On Mon, 1 Feb 2010, Roman Petrenko wrote:

> 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
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:41 CST