From: regafan_at_usc.es
Date: Thu Mar 15 2007 - 15:06:16 CDT
Hello,
I have another problem about trajectories from NAMD to be used in the
analysis with Charmm. With NAMD, the simulation was done by steps, and
I don´t have only one trajectory file for all the simulation, but
several files that I have treated with ptraj to get a total
trajectory. When this trajectory is used in CHARMM, the program only
recognizes the first individual one, and the loop used in the script
stops.
Do you have a solution for doing that Charmm reads all the steps of
the trajectory?
The script for analysis is:
...
open read card name "top_all22_prot.inp" unit 20
read rtf card unit 20
close unit 20
open read card name "par_all22_prot.inp" unit 20
read parameter card unit 20
close unit 20
!open and read psf file
open read card name "4f2hc_rx.psf" unit 20
read psf card unit 20
close unit 20
!Set up for reading coordinate sets from trajectory and writing energy data
open write card name "energy.tst" unit 52
open read file name trayectoria_10ns.dcd unit 51
trajectory query unit 51
trajectory iread 51 begin ?start skip ?skip
set i 1
!Loop for reading coordinate sets and calculating an interaction energy.
label loop
trajectory read
update
interaction select segid pro1 .and. resid 1 : 416 end -
select segid pro2 .and. resid 417 : 837 end unit 52
increment i
if i le ?nfile goto loop
stop
...
Thank you very much for your help,
Rebeca García
Post-doctoral student
Barcelona
Spain
Citando regafan_at_usc.es:
>
> Thank you very much, Alessandro.
> You were right, I had run NAMD on a computer of different endianness of
> the computer on which I was analyzing the trajectory with Charmm. Now,
> it works without any format conversion.
> Thanks!
>
> Rebeca García
> Post-doctoral student
> Barcelona
> Spain
>
>
>
>
>
>
>
>
>
> Citando Alessandro Cembran <cembran_at_chem.umn.edu>:
>
>> Rebeca,
>>
>> I've been running NAMD and post processing the trajectories with CHARMM
>> as well and I've never run into any problem.
>> In some cases, one might have to pay attention to the orientation of
>> the box (I am thinking about hexagonal cells, that need to be rotated
>> by 15 degrees around the Z axis) but the raw numbers are always read
>> correctly.
>> Another thing that I can think of is that you might have run NAMD on a
>> computer of different endianness of the computer on which you are
>> analyzing the trajectory. If this is the case, you might
>> a) Recompile CHARMM with TESTENDIAN in the pref.dat (never tried this one)
>> b) Change the endianness of the shell on which you are running CHARMM
>> to match the original one:
>> export F_UFMTENDIAN=little or ...=big
>> c) Compile and run CHARMM on the machine the trajectories have been
>> produced.
>>
>> If none of the two cases applies to your problem, then could you be
>> more specific about what is the compatibility issue?
>>
>> Alessandro
>>
>> regafan_at_usc.es wrote:
>>> Hello,
>>> I have done a simulation of a protein with NAMD, using the Charmm
>>> force field, and now I would like to perform an analysis with
>>> CHARMM.
>>> I have problems of compatibility of the trajectory files obtained
>>> with NAMD and CHARMM. Does anyboy knows how to convert a dcd
>>> trajectory file from NAMD to the correct one used by Charmm?
>>>
>>> Thanks a lot!
>>>
>>> Rebeca García
>>> Post-doctoral student
>>> Barcelona
>>> Spain
>>>
>>>
>>
>>
>> --
>> Alessandro Cembran,PhD
>> Post Doctoral Associate
>> Mailing Address:
>> Univ. of Minnesota, Dept. of Chemistry
>> G2, 139 Smith Hall 207 Pleasant St SE
>> Minneapolis, MN 55455-0431
>> Office:
>> Univ. of Minnesota, Walter Library
>> 117 Pleasant St SE, Room 473
>> Phone: +1 612-624-4617
>> E-mail: cembran_at_chem.umn.edu
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:28 CST