Re: [gmx-users] rerun on gro file
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
00.00.0
Grid: 9 x 9 x 9 cells
Energies (kJ/mol)
AngleProper Dih. LJ-14 Coulomb-14LJ (SR)
5.86630e+035.17677e+033.00597e+031.71532e+043.14231e+04
Coulomb (SR) Coul. recip. PotentialKinetic En. Total Energy
-2.38136e+05 -7.84053e+04 -2.53916e+050.0e+00 -2.53916e+05
Temperature Pressure (bar) Cons. rmsd ()
0.0e+001.62084e+040.0e+00
Step Time Lambda
0 50.00.0
Energies (kJ/mol)
AngleProper Dih. LJ-14 Coulomb-14LJ (SR)
5.76066e+035.05958e+032.98882e+031.71326e+043.15995e+04
Coulomb (SR) Coul. recip. PotentialKinetic En. Total Energy
-2.39283e+05 -7.85130e+04 -2.55255e+050.0e+00 -2.55255e+05
Temperature Pressure (bar) Cons. rmsd ()
0.0e+001.61866e+040.0e+00
Step Time Lambda
0 100.00.0
Energies (kJ/mol)
AngleProper Dih. LJ-14 Coulomb-14LJ (SR)
5.87814e+035.08816e+033.04501e+031.72935e+043.20109e+04
Coulomb (SR) Coul. recip. PotentialKinetic En. Total Energy
-2.38788e+05 -7.85518e+04 -2.54024e+050.0e+00 -2.54024e+05
Temperature Pressure (bar) Cons. rmsd ()
0.0e+001.62936e+040.0e+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 //* wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] rerun on gro file
To: "Discussion list for GROMACS users"
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
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Re: [gmx-users] rerun on gro file
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 0.0 0.0 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 0.0e+00 -2.53916e+05 Temperature Pressure (bar) Cons. rmsd () 0.0e+00 1.62084e+04 0.0e+00 Step Time Lambda 0 50.0 0.0 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 0.0e+00 -2.55255e+05 Temperature Pressure (bar) Cons. rmsd () 0.0e+00 1.61866e+04 0.0e+00 Step Time Lambda 0 100.0 0.0 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 0.0e+00 -2.54024e+05 Temperature Pressure (bar) Cons. rmsd () 0.0e+00 1.62936e+04 0.0e+00 Step is always zero !!! do you think is this the problem ?!! Fahimeh --- On Sat, 9/18/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] rerun on gro file To: "Discussion list for GROMACS users" 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] rerun on gro file
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] rerun on gro file
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 ?!! Fahimeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
