Hi Patrick,<br>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?<br> <br>Ciao,<br>Otto<br><br><div class="gmail_quote">
On Tue, Dec 13, 2011 at 1:23 PM, Patrick Fuchs <span dir="ltr"><<a href="mailto:patrick.fuchs@univ-paris-diderot.fr">patrick.fuchs@univ-paris-diderot.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi Otto,<br>
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.<br>
I think this is the standard flow for REMD as explained in: <a href="http://www.gromacs.org/Documentation/How-tos/REMD" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/REMD</a>. The only difference is that you use a different lambda value, so a different Hamiltonian, instead of a different temperature for each replica.<br>
Ciao,<br>
<br>
Patrick<br>
<br>
Le 13/12/2011 11:46, Otto Master a écrit :<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi Patrick,<div class="im"><br>
thanks for your help. What I still do not understand is, how I can<br>
set-up the replica simulation starting from the two equilibrated<br>
systems. What do I have to put into the .mdp file and in the grompp<br>
command to consider the two equilibrated configurations and further<br>
obtain the tpr files for the different replica for different lambda<br>
values to interpolate between the two configuration. I would be very<br>
glad if you could help me on that.<br>
<br>
All the best<br>
Otto<br>
<br>
On Mon, Dec 12, 2011 at 1:50 PM, Patrick Fuchs<br>
<<a href="mailto:patrick.fuchs@univ-paris-diderot.fr" target="_blank">patrick.fuchs@univ-paris-<u></u>diderot.fr</a><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:patrick.fuchs@univ-paris-diderot.fr" target="_blank">patrick.fuchs@univ-<u></u>paris-diderot.fr</a>>> wrote:<br>
<br>
Hi Otto,<br>
yes I copied those two files you mentionned (also .rtp for charges)<br>
in some specific directory to apply the appropriate scaling. But<br>
according to the authors this REST implementation, you just need<br>
that for the highest "temperature" (for the lowest, the Hamiltonian<br>
is unchanged) and then intermediate "temperatures" are interpolated<br>
using the lambda factor. So for equilibrating each replica, you just<br>
need to set the appropriate lambda value.<br>
Now I'd consider Mark's advice to use the -pp flag of grompp which<br>
might be convenient for scripting the scaling of the potential.<br>
Ciao,<br>
<br>
Patrick<br>
<br>
Le 12/12/2011 12:56, Otto Master a écrit :<br>
<br>
Hi Patrick,<br>
Thanks a lot for your reply. Just to be sure, you create for<br>
every replicate a copy of the original force field, and after<br>
you manipulate the parameter in ffnonbonded.itp and<br>
ffbonded.itp. Then you go for each replicate through the usual<br>
simulation preparation steps (minimisation, nvt, equilibration<br>
...). The result of this you use for the replicate exchange<br>
simulation.<br>
<br>
Thanks a lot<br>
Otto<br>
<br>
On 12 Dec 2011, at 10:42, Patrick<br></div></div>
Fuchs<<a href="mailto:patrick.fuchs@univ-__paris-diderot.fr" target="_blank">patrick.fuchs@univ-__<u></u>paris-diderot.fr</a><br>
<mailto:<a href="mailto:patrick.fuchs@univ-paris-diderot.fr" target="_blank">patrick.fuchs@univ-<u></u>paris-diderot.fr</a>>> wrote:<div><div></div><div class="h5"><br>
<br>
Hi Otto,<br>
in my lab we tried to implement this REST variant in GROMACS<br>
as proposed by those authors. We figured out that it was<br>
easier to manipulate directly the parameters files in the<br>
top directory. There you know exactly what you are doing;<br>
recall that some interactions (i.e. solvent/solvent) mustn't<br>
be scaled whereas some others have to be scaled<br>
(solute/solute and solute/solvent).<br>
It's probably possible to do it in the tpr file, but it<br>
looked less trivial to me: i) you have to know how atoms are<br>
coded in the file (e.g. in the functype[???]=LJ_SR[...]<br>
matrix, you have to understand how atom numbers are coded<br>
there), ii) you have to regenerate a tpr from plain text<br>
file; it's probably doable, but I don't know how. Actually,<br>
maybe some developers can tell if it's possible.<br>
Good luck,<br>
<br>
Patrick<br>
<br>
Le 08/12/2011 19:01, Otto Master a écrit :<br>
<br>
Dear gromacs users,<br>
<br>
Recently I stumbled over following paper:<br>
T. Terakawa, T. Kameda, and S. Takada, On Easy<br>
Implementation of a<br>
Variant of the Replica Exchange with Solute Tempering in<br>
GROMACS.<br>
Journal of Computational Chemistry 32 (2011) 1228-1234.<br>
<br>
The authors suggested an easy way to run this kind of<br>
simulation with<br>
Gromacs, without even changing the code. The only thing<br>
that is need, is<br>
the the rescaling of the parameters in the parameter<br>
file. Since the<br>
reduction of the replica number is quite appealing to me<br>
I wonder which<br>
file I have to change? Actually, I thought of<br>
manipulating the .tpr file<br>
or to rescale and creating the force fields for every<br>
replicate. Is this<br>
feasible, or is there a better way?<br>
<br>
Manipulating the .tpr file could be easier, since it<br>
unifies (right?)<br>
the parameters from the different force fields, before<br>
sending it to the<br>
mdrun application. But for this I would like to<br>
understand the tpr file<br>
first.There are quite a lot of entries and first I try<br>
to understand LJ<br>
interactions and how they are defined in this file. I<br>
found two entries<br>
<br>
LJ14<br>
functype[154]=LJ14, c6A= 0.00000000e+00, c12A=<br>
0.00000000e+00,<br>
c6B= 0.00000000e+00, c12B= 0.00000000e+00<br>
functype[155]=LJ14, c6A= 4.46680887e-03, c12A=<br>
4.74702711e-06,<br>
c6B= 4.46680887e-03, c12B= 4.74702711e-06<br>
<br>
which corresponds to following interactions<br>
<br>
LJ-14:<br>
nr: 876<br>
iatoms:<br>
0 type=154 (LJ14) 0 4<br>
1 type=155 (LJ14) 0 5<br>
<br>
When I tried to calculate the parameters from the<br>
combination rules (in<br>
this case Gromos 53A6 force field), I found (the<br>
highlighted columns<br>
contain the original parameters for the specific atom<br>
groups from the<br>
Gromos documentation and the calculated value for<br>
combining the two<br>
parameters:<br>
<br>
<br>
<br>
<br>
sqrt(C6i) (from ff) sqrt(C6j) (from ff)<br>
sqrt(C6i)*sqrt(C6j) value<br>
from tpr file<br>
functype[154]=LJ14, c6A= CH3 H 0.09805 0<br>
0 0.00E+00<br>
functype[155]=LJ14, c6A= CH3 CH1 0.09805<br>
0.0779 0.007638095 4.47E-03<br>
functype[156]=LJ14, c6A= C CH2 0.04838<br>
0.08642 0.004181 3.33E-03<br>
functype[157]=LJ14, c6A= C C 0.04838<br>
0.04838 0.002340624 2.34E-03<br>
<br>
<br>
The values for N, C, O, H seems to be OK, but I have<br>
problems to get the<br>
same value, when CH1, CH2, CH3 are involved. Since I do<br>
not have too<br>
much experience, I would like to know how the value from<br>
the .tpr file<br>
can be derived.<br>
<br>
The other entry for LJ potential is the short range term<br>
LJ_SR (.tpr file<br>
<br>
ffparams:<br>
atnr=11<br>
ntypes=170<br>
functype[0]=LJ_SR, c6= 9.61380266e-03, c12=<br>
2.66462448e-05<br>
functype[1]=LJ_SR, c6= 4.74365894e-03, c12=<br>
1.14699596e-05<br>
functype[2]=LJ_SR, c6= 4.66325786e-03, c12=<br>
5.16199998e-06<br>
<br>
Unfortunately, I do not find the section where the<br>
function is assigned<br>
to a specific pair of interaction. Where are these<br>
functions assigned to<br>
a specific interaction? Furthermore, is it possible to<br>
distinguish<br>
between intra-nonbonded (solute-solute) and inter-bonded<br>
(water-solute)<br>
interaction?<br>
<br>
For you this might be an easy question to answer, and<br>
you immediately<br>
realize there is a beginner at work, but nevertheless I<br>
would appreciate<br>
any help.<br>
<br>
All the best<br>
Otto<br>
<br>
<br>
<br>
--<br></div></div>
______________________________<u></u>______________________________<u></u>_______________<div class="im"><br>
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Dynamique des Structures et Interactions des Macromolécules<br>
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______________________________<u></u>______________________________<u></u>___________<br>
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