Hi Patrick,
again thanks a lot for your valuable help. But I do not get my head
around how to tell grompp that for lambda=0 I would like to use the the
unscaled Hamiltonian and for lambda=1 the highest "temperature". In the
tutorial the change in temperature is a number which is passed to the
pre-processor, but for REST a number (lambda=0 and lambda=1) corresponds
to different topology, which are written in a file. I do not know how to
specify that. What is the identifier or should I pass something
additionally to grompp, referring to the two topology files?
Ciao,
Otto
On Tue, Dec 13, 2011 at 1:23 PM, Patrick Fuchs
<patrick.fu...@univ-paris-diderot.fr
<mailto:patrick.fu...@univ-paris-diderot.fr>> wrote:
Hi Otto,
you have to equilibrate at each lambda value! The unscaled
Hamiltionian is your lowest "temperature", say 300K, which
corresponds to lambda=0. You generate the highest "temperature" by
appropriately scaling the Hamiltonian, say 600K, which corresponds
to lambda=1. Then you create n directories, one for each replica. In
each directory, you set a different lambda value from 0 to 1 in the
mdp file and you equilibrate each replica. At the end, you obtain n
gro files that can serve as input to generate n tpr files for the
REMD run.
I think this is the standard flow for REMD as explained in:
http://www.gromacs.org/__Documentation/How-tos/REMD
<http://www.gromacs.org/Documentation/How-tos/REMD>. The only
difference is that you use a different lambda value, so a different
Hamiltonian, instead of a different temperature for each replica.
Ciao,
Patrick
Le 13/12/2011 11:46, Otto Master a écrit :
Hi Patrick,
thanks for your help. What I still do not understand is, how I can
set-up the replica simulation starting from the two equilibrated
systems. What do I have to put into the .mdp file and in the grompp
command to consider the two equilibrated configurations and further
obtain the tpr files for the different replica for different lambda
values to interpolate between the two configuration. I would be very
glad if you could help me on that.
All the best
Otto
On Mon, Dec 12, 2011 at 1:50 PM, Patrick Fuchs
<patrick.fuchs@univ-paris-__diderot.fr
<mailto:patrick.fu...@univ-paris-diderot.fr>
<mailto:patrick.fuchs@univ-__paris-diderot.fr
<mailto:patrick.fu...@univ-paris-diderot.fr>>> wrote:
Hi Otto,
yes I copied those two files you mentionned (also .rtp for
charges)
in some specific directory to apply the appropriate scaling. But
according to the authors this REST implementation, you just need
that for the highest "temperature" (for the lowest, the
Hamiltonian
is unchanged) and then intermediate "temperatures" are
interpolated
using the lambda factor. So for equilibrating each replica,
you just
need to set the appropriate lambda value.
Now I'd consider Mark's advice to use the -pp flag of grompp
which
might be convenient for scripting the scaling of the potential.
Ciao,
Patrick
Le 12/12/2011 12:56, Otto Master a écrit :
Hi Patrick,
Thanks a lot for your reply. Just to be sure, you create for
every replicate a copy of the original force field, and
after
you manipulate the parameter in ffnonbonded.itp and
ffbonded.itp. Then you go for each replicate through the
usual
simulation preparation steps (minimisation, nvt,
equilibration
...). The result of this you use for the replicate exchange
simulation.
Thanks a lot
Otto
On 12 Dec 2011, at 10:42, Patrick
Fuchs<patrick.fuchs@univ-____paris-diderot.fr
<mailto:patrick.fuchs@univ-__paris-diderot.fr>
<mailto:patrick.fuchs@univ-__paris-diderot.fr
<mailto:patrick.fu...@univ-paris-diderot.fr>>> wrote:
Hi Otto,
in my lab we tried to implement this REST variant in
GROMACS
as proposed by those authors. We figured out that it was
easier to manipulate directly the parameters files
in the
top directory. There you know exactly what you are
doing;
recall that some interactions (i.e. solvent/solvent)
mustn't
be scaled whereas some others have to be scaled
(solute/solute and solute/solvent).
It's probably possible to do it in the tpr file, but it
looked less trivial to me: i) you have to know how
atoms are
coded in the file (e.g. in the functype[???]=LJ_SR[...]
matrix, you have to understand how atom numbers are
coded
there), ii) you have to regenerate a tpr from plain text
file; it's probably doable, but I don't know how.
Actually,
maybe some developers can tell if it's possible.
Good luck,
Patrick
Le 08/12/2011 19:01, Otto Master a écrit :
Dear gromacs users,
Recently I stumbled over following paper:
T. Terakawa, T. Kameda, and S. Takada, On Easy
Implementation of a
Variant of the Replica Exchange with Solute
Tempering in
GROMACS.
Journal of Computational Chemistry 32 (2011)
1228-1234.
The authors suggested an easy way to run this
kind of
simulation with
Gromacs, without even changing the code. The
only thing
that is need, is
the the rescaling of the parameters in the parameter
file. Since the
reduction of the replica number is quite
appealing to me
I wonder which
file I have to change? Actually, I thought of
manipulating the .tpr file
or to rescale and creating the force fields for
every
replicate. Is this
feasible, or is there a better way?
Manipulating the .tpr file could be easier, since it
unifies (right?)
the parameters from the different force fields,
before
sending it to the
mdrun application. But for this I would like to
understand the tpr file
first.There are quite a lot of entries and first
I try
to understand LJ
interactions and how they are defined in this
file. I
found two entries
LJ14
functype[154]=LJ14, c6A=
0.00000000e+00, c12A=
0.00000000e+00,
c6B= 0.00000000e+00, c12B= 0.00000000e+00
functype[155]=LJ14, c6A=
4.46680887e-03, c12A=
4.74702711e-06,
c6B= 4.46680887e-03, c12B= 4.74702711e-06
which corresponds to following interactions
LJ-14:
nr: 876
iatoms:
0 type=154 (LJ14) 0 4
1 type=155 (LJ14) 0 5
When I tried to calculate the parameters from the
combination rules (in
this case Gromos 53A6 force field), I found (the
highlighted columns
contain the original parameters for the specific
atom
groups from the
Gromos documentation and the calculated value for
combining the two
parameters:
sqrt(C6i) (from ff) sqrt(C6j) (from ff)
sqrt(C6i)*sqrt(C6j) value
from tpr file
functype[154]=LJ14, c6A= CH3 H
0.09805 0
0 0.00E+00
functype[155]=LJ14, c6A= CH3 CH1 0.09805
0.0779 0.007638095 4.47E-03
functype[156]=LJ14, c6A= C CH2 0.04838
0.08642 0.004181 3.33E-03
functype[157]=LJ14, c6A= C C 0.04838
0.04838 0.002340624 2.34E-03
The values for N, C, O, H seems to be OK, but I have
problems to get the
same value, when CH1, CH2, CH3 are involved.
Since I do
not have too
much experience, I would like to know how the
value from
the .tpr file
can be derived.
The other entry for LJ potential is the short
range term
LJ_SR (.tpr file
ffparams:
atnr=11
ntypes=170
functype[0]=LJ_SR, c6= 9.61380266e-03,
c12=
2.66462448e-05
functype[1]=LJ_SR, c6= 4.74365894e-03,
c12=
1.14699596e-05
functype[2]=LJ_SR, c6= 4.66325786e-03,
c12=
5.16199998e-06
Unfortunately, I do not find the section where the
function is assigned
to a specific pair of interaction. Where are these
functions assigned to
a specific interaction? Furthermore, is it
possible to
distinguish
between intra-nonbonded (solute-solute) and
inter-bonded
(water-solute)
interaction?
For you this might be an easy question to
answer, and
you immediately
realize there is a beginner at work, but
nevertheless I
would appreciate
any help.
All the best
Otto
--
_______________________________________________________________________________
Patrick FUCHS
Dynamique des Structures et Interactions des
Macromolécules
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INTS, INSERM UMR-S665, Université Paris Diderot,
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