[gmx-users] problem about rmsd
bharat v. adkar
bharat at sscu.iisc.ernet.in
Fri Mar 21 20:18:57 CET 2008
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
> You didn't tell tpbconv how long to continue the simulation. Use tpbconv -until
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.
>> 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
>> 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
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