Jamie Seyed wrote:
Hi Justin,
Thanks for your complete answer. Actually I have another question here.
It is about potential energy after mdrun. From md.log in AVERAGES
section I have potential=8.81e+04 !!! and it is 9.3e+04 from em.log the
same order. Can I trust these results or I did something wrong? Is it
always the same order for different systems? Can you please give me some
advice about it?? Many Thanks in Advance/ Jamie
I don't know anything about your system, so it's hard to make a generalization.
Positive values of potential indicate repulsive or unsatisfied interactions.
If you're running your system in solvent, I would think something is wrong;
vacuum might be a different story, but I don't usually do vacuum simulations, so
I don't have any real expertise here.
-Justin
On Sat, Aug 15, 2009 at 6:37 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Jamie Seyed wrote:
Hi,
How can I make sure that position restraint is actually applied
(after grompp & mdrun)? When I grep "POSRES" or "posres" I can
not see any information... Many Thanks in Advance/Jamie
If your topology has the appropriate #ifdef POSRES, and you have
"define = -DPOSRES" in your .mdp file, then it worked :) Position
restraints are applied during mdrun, and show up in the .log file as
"Position Rest." entries.
-Justin
On Fri, Aug 14, 2009 at 9:07 PM, Mark Abraham
<[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> wrote:
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
<[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>>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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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