Jamie Seyed wrote:
Hi Mark,
Thanks for the answers. One question still remains for me: in the fws
tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run
grompp followed by mdrun... Am I missing some thing? Because I can not see
it introduces something that to be restrained..?? Would you please let me
know what I am missing here?? Many Thanks in Advance/Jamie
pdb2gmx automatically produces a posre.itp file, whose position
restraint contents are #included from the .top file it produces, and
whose function is sensitive to the -DPOSRES option. Search the wiki for
discussion of this machinery.
Mark
On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
Jamie Seyed wrote:
Dear all,
I have questions regarding the position restrain md. I tried to find the
answer of my questions from the mailing list, but it is not clear yet.
In the fws tutorial when it says (in the pr.mdp)
tc_grps=Protein non-protein
(1) Doesn't that mean everything in the system? I think for this case we
can
simply write "system" because system is made by protein and non-protein??
It includes the whole system, but it is often a good idea not to couple
groups of heterogeneous heat capacity to the same thermostat. That said, if
the groups are too small, you get other problems. See also
http://oldwiki.gromacs.org/index.php/temperature_coupling
(2) In this case how program recognize which one should restrain and which
one not, because it included all??
Temperature coupling has no linkage with position restraints. You defined
the latter in your .top file.
(3) This step is required for every system or only proteins??
It may or may not be useful in achieving stable equilibration for any
system. See
http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
(4) If I want to make an index file and I specify a group that need to be
constrained, in the generated index file I will get system and all its
parts
and an extra part for my specific part that need to be constrain...Is that
ok??
"constraints" are different from "restraints" in GROMACS usage. make_ndx
does allow you to generate new index groups, but you will need to (re-)read
the relevant manual sections to understand that neither of these algorithms
uses index groups. (Or to prove my memory wrong!)
(5) In my case I have a molecule (MOL) and water (SOL), for position
restrain md should I use "tc_grps=MOL SOL" (according to fws tutorial)
or
I need only write "tc_grps=MOL"?? Many Thanks in Advance/Jamie
The latter won't work, for all atoms must be members of a
temperature-coupling group if any are.
What you actually need is a clear understanding of your strategic
objective. Hopefully some of the links will move you towards that.
Mark
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