[gmx-users] rerun on gro file

[Justin A. Lemkul]

fahimeh baftizadeh wrote:
> 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 ?!!
> 

Since I don't exactly know what you're doing, I can't say for sure.  Most 
analyses are conducted using the time, not the step.  If you're trying to 
analyze only 100 ps of data, it shouldn't be that difficult to re-create a real 
.xtc trajectory, right?

-Justin

> 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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> 

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

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

========================================