[gmx-users] problem about rmsd

bharat v. adkar bharat at sscu.iisc.ernet.in
Fri Mar 21 20:18:57 CET 2008

dear sudheer,

On Fri, 21 Mar 2008, Justin A. Lemkul wrote:

> Quoting sudheer babu <sudheer.pbm07 at gmail.com>:
>> Thanks for your reply,
>> I am mentioning commands, from crashing the simulation
>> 1. tpbconv  -f  protein.trr  -s protein.tpr -e protein.edr -n index.ndx -o
>> out.tpr
> You didn't tell tpbconv how long to continue the simulation.  Use tpbconv -until
> 1000

check whether your original mdp file mentions nsteps correctly which, in 
your case, should correspond to 1000 ps and not 900 ps (which most 
probably will be corresponding to 1000 ps).

tpbconv without -until option should be okay. you should get a tpr which 
will run your simulation from the time it has got crashed to 1000 ps.

> -Justin
>> 2.mdrun -v -deffnm -o out.tpr
>> 3.trjcat -f 633ps_pro.xtc 1ns_pro.xtc -settime -o
>>   it asked time I mentioned  0 and 633, then it shown that 900ps trajectory
>> files wirte into trjout.xtc

if nsteps in original mdp corresponds to 1000 ps, then it seems that while 
inputting the time for second xtc, you are making some mistake. are you 
sure that it has got crashed at 633 ps. just check it by running gmxcheck 
on previous xtc.
alternatively, run trjcat again with the same flags, but now while 
inputting time for second xtc, input 'c' instead of exact time. it will 
automatically check where to start renumbering the time from.


>> 4.g_rms -f trjout.xtc -s em_wat.gro -pbc -o 1ns_rmsd
>> 5. by using this plotted graph it shown values till 900ps on x-axis in
>> gnuplot
>> is there any way to get 1000ps simulation values?
>> Thanks in advance.
> ========================================
> Justin A. Lemkul
> Graduate Research Assistant
> 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 at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

More information about the gromacs.org_gmx-users mailing list