[gmx-users] Fw: asking guidance

Smith, Micholas D. smithmd at ornl.gov
Fri Mar 9 20:53:44 CET 2018

Add the -sep flag that will split the writting into multiple files instead of 1 large pdb. Alternatively you could script up a spliting program with something like awk 

awk 'BEGIN{filename="MyFile_"i".pdb"}{print $0>filename; if $0~/ENDMDL/; i++;filename="MyFile_"i".pdb"}}' 


Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mansoureh Shahbazi <shahbazi.2010 at rocketmail.com>
Sent: Friday, March 09, 2018 11:13 AM
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Fw: asking guidance

Dear director,I am using Gromacs package to perform MD simulations and I have a 100 ns long MD simulation. For the further assays, I must split this 100 ns trajectory into 100 pdb files (to get one pdf file from each 1000 ps or 1 ns of simulation).

I have found two commands:
gmx trjconv -s topol.tpr -f md_0_1.xtc -dt 1000 -o trj.pdb
gmx trjconv –f md.xtc –s md.tpr –b 1 –e 1000 –o md.pdb (and -b 1001 -e 2000 and so on )

I tried both of them. But for the first one, I got only one pdb file and for the second command, I have to repeat the command 100 times to get them and furthermore I am not sure it gives the correct results.  Can you please tell me is there any command to split the 100 ns trajectory with the time intervals of 1000 ps and get 100 pdb files at one time?  If no, please make me aware that is the second command gives the true result?  I am looking forward to your answer, Thanks in advance for your guidance,Sincerely yours,Mansoureh

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