[gmx-users] rerun on gro file

[fahimeh baftizadeh]

Thank you Justin,

I used -settime option and set different starting time, at the end I check xtc file with gmxcheck and the number of fram is ok. 
But I still have the same problem, I copy what is inside the log file:

  Step           Time         Lambda
              0        0.00000        0.00000

Grid: 9 x 9 x 9 cells
   Energies (kJ/mol)
          Angle    Proper Dih.          LJ-14     Coulomb-14        LJ (SR)
    5.86630e+03    5.17677e+03    3.00597e+03    1.71532e+04    3.14231e+04
   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.   Total Energy
   -2.38136e+05   -7.84053e+04   -2.53916e+05    0.00000e+00   -2.53916e+05
    Temperature Pressure (bar)  Cons. rmsd ()
    0.00000e+00    1.62084e+04    0.00000e+00

           Step           Time         Lambda
              0       50.00000        0.00000

   Energies (kJ/mol)
          Angle    Proper Dih.          LJ-14     Coulomb-14        LJ (SR)
    5.76066e+03    5.05958e+03    2.98882e+03    1.71326e+04    3.15995e+04
   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.   Total Energy
   -2.39283e+05   -7.85130e+04   -2.55255e+05    0.00000e+00   -2.55255e+05
    Temperature Pressure (bar)  Cons. rmsd ()
    0.00000e+00    1.61866e+04    0.00000e+00

           Step           Time         Lambda
              0      100.00000        0.00000

   Energies (kJ/mol)
          Angle    Proper Dih.          LJ-14     Coulomb-14        LJ (SR)
    5.87814e+03    5.08816e+03    3.04501e+03    1.72935e+04    3.20109e+04
   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.   Total Energy
   -2.38788e+05   -7.85518e+04   -2.54024e+05    0.00000e+00   -2.54024e+05
    Temperature Pressure (bar)  Cons. rmsd ()
    0.00000e+00    1.62936e+04    0.00000e+00

Step is always zero !!! do you think is this the problem ?!!

Fahimeh
--- On Sat, 9/18/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] rerun on gro file
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Saturday, September 18, 2010, 10:51 PM



fahimeh baftizadeh wrote:
> Hi,
> 
> I'm trying to do rerun on a trajectory which came from catting some gro files of a metadynamics simulation. I simply did trjcat -f 1.gro 2.gro 3.gro -o all.xtc -cat
> then I used this all.xtc for rerun.
> the output COLVAR is written but only for one step, I did test on some other trajectory and I am sure that META_INP.dat which is the input of metadynamics is correct.
> I dont know if the problem is catting the gro file ?!!
> 

Probably.  Use -settime to assign times to each of the frames, otherwise they may all be set to something like 0 or -1.  You can use gmxcheck on the .xtc file to see what Gromacs thinks it contains.

-Justin

> Fahimeh 
> 

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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