[gmx-users] combine two gro files

[Dallas Warren]

Why is it that you want to combine the two coordinate files?

md.gro is the coordinates of the system at the end of 20ns.

md_extend.gro is the coordinates of the system at the end of 22ns.

So combining them will not make much sense.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Nur Syafiqah Abdul Ghani
> Sent: Wednesday, 13 March 2013 2:10 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] combine two gro files
> 
> Hi all,
> 
> I just finished my simulation protein in mix solvent with the file
> name md.gro but when i analyze the protein it seems not stable yet
> therefore i have to extend it about 2ns more.The previously i used
> 20ns for my simulation.So the extended oneis name md_extend.gro and
> also the others file, trr tpr.
> 
> The command that i used to extend the simu is like below :
> tpbconv -f md.trr -s md.tpr -o md_extend.tpr -extend 2000
> mdrun -v -cpi md.cpt -deffnm md_extend
> 
> >From what I understand the new file that created after extend is only
> 2ns second.right?
> How i can combine the gro file from the original and the extended one?
> Because the xtc trr and also edr file i combine it by using comand
> trjcat and eneconv.
> 
> The trjcat cant combine the gro file because the error stated :
> Fatal error:
> Can not write a gro file without atom names
> 
> So anyone facing this problems.?I already search in previous problem
> but they said convert the gro to pdb?then use command cat..can i use
> that?
> 
> --
> Best Regards,
> 
> Nur Syafiqah Abdul Ghani,
> Theoretical and Computational Chemistry Laboratory,
> Department of Chemistry,
> Faculty of Science,
> Universiti Putra Malaysia,
> 43400 Serdang,
> Selangor.
> alternative email : syafiqahabdulghani at gmail.com
> --
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