On 1/10/10 12:08 AM, pavan payghan wrote:
HI
I want to run my system for almost 50 ns but as diskspace
becomes almost full to run system for this much time
so which of the option u suggest
1. Giving 10ns with each run by .mdp option .
2. giving full run of 50ns and then creating at each time new
tpr file to continue run for next step while storing .xtc
at each step and concurrent removal of .trr file as it
occupies a lots of diskspace.
While restarting run by using tpbconv to create new .tpr file for
new run may i know following of which commond is
correct
1. tpbconv -s md1_out.tpr -o md2_out.tpr -e md1_out.edr
2 tpbconv -s md1_out.tpr -o md2_out.tpr -e md1_out.edr
-extend 8000.
I don't know what #1 would actually be doing; seems like nothing.
tell me what -extends signifies i.e.point from where you
want to continue or extend the given number of steps.
From tpbconv -h:
"-extend real 0 Extend runtime by this amount (ps)"
im asking this because when i run it using previous (1) commend i
got run in which the middle portion was
containing no information about run.
that is system run well till 7 ns then i killed run to continue
it for seond time this time it run well but at the end
i found that 7ns - 13ns portin was not there, why it is so?
( may it be the reason because some incomplete frames are present .)
also
tell me which is the best way to check whether the system is
running well or not .?
I think you need to read about the checkpointing feature, it simplifies all of
this immensely:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Very simple.
regarding g_rms
While selecting groups for RMSD which is correct
1. select whole system with solvent
2. select only molecule of interest .
The selection depends on which step you're talking about (least squares fitting
or actual calculation). See below. I doubt you ever want to consider solvent
for anything, though (assuming you're simulating some "normal" protein system).
also while choosing groups is it correct to choose both time i.e.
for least square fitting and RMSD same groups.
It certainly can be, depending on which groups you want to use for the fitting.
Best to do some background reading on what these algorithms are doing before
just haphazardly making choices :)
-Justin
Thanking you in Advance.
Mr. Pavan Payghan
INDIAN INSTITUTE OF CHEMICAL BIOLOGY
KOLKATA
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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