[gmx-users] there wasn't md_0_1.xtc file

marzieh dehghan dehghanmarzieh at gmail.com
Wed Apr 15 05:58:37 CEST 2015

Hi every body

I have two questions?

1- accroding to the previos email, I used gromacs to run a covalent bond,
for the first try,I run my covalent bond based on the tutorail (lysozyme in
water) that nstxtcout = 0 was in md.mdp file,
so I changed nstxtcout =0 to >0 and run was repeated. in the both try, I
didn't achieve md_0_1.xtc.

*I would like to know which parameters I should  change to obtain this
2- after finishing 1ns, I have several pdb files such as step0c.pdb,
step1c.pdb, step1b.pdb, step2b.pdb, step2c.pdb.

*please let me know I can use thses pdb files as a result?*

 thanks a lot

best wishes

*Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
Biophysics (IBB)University of Tehran, Tehran- Iran.*

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