From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Mar 15 2007 - 16:20:40 CDT
Hi Rebeca,
Just out of curiosity... I saw in your CHARMM script that you're
trying to calculate interaction energies. Is that correct? If so, have
you tried to use the energy plugin of VMD? You might find it useful.
If you want to calculate other things, there are plenty of small
analysis tools included in GROMACS (Sorry guys, but I like them!).
Michel
2007/3/15, Peter Freddolino <petefred_at_ks.uiuc.edu>:
> You could use catdcd to put all the dcds together into one before your
> analysis; that's probably the best bet.
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
> Peter
>
> regafan_at_usc.es wrote:
> > I mean the first trajectory (it has 40 frames). I suppose Charmm read
> > the "total"
> > trajectory I have created with ptraj and asumes that it only has 40
> > frames. The total
> > frames I have are 1068.
> > Do you have any idea of how Charmm can read all the frames?
> >
> >
> >
> >
> > Citando Peter Freddolino < petefred_at_ks.uiuc.edu>:
> >
> >> By the "first individual one", do you mean the first frame, or the first
> >> trajectory?
> >>
> >> Peter
> >>
> >> regafan_at_usc.es wrote:
> >>>
> >>> 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
> >>>
> >>>
> >>
> >
> >
>
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