I achieve <br><br>Steepest Descents converged to machine precision in 205 steps,<br>but did not reach the requested Fmax < 10.<br>Potential Energy = -1.49131940478719e+07<br>Maximum force = 1.09664530279637e+06 on atom 1520 (parto of the protein)<br>
Norm of force = 2.28369808518165e+06<br><br>and the system looked with vmd doesn't look as if it was exploding. However, I have warnings about the table extension and I don't know why but gromacs writes pdb files sometime. However I thought that there might have been an error in the way I defined the position restraints, in fact in the mdp file I hade define = -DEPOSRE while in the topology I had ifdef DEFINE_WAT, so it might have moved it all without fixing the water. So I tried again and this time I got <br>
<br>Steepest Descents converged to machine precision in 72 steps,<br>but did not reach the requested Fmax < 10.<br>Potential Energy = -2.0135496e+07<br>Maximum force = 2.0486184e+12 on atom 4479<br>Norm of force = 7.2424045e+13<br>
<br>but again the same issue with table extent and still the production of pdb files. <br><br>Any explanations?<br><br>Thanks<br>Francesca<br><br><br><br><div class="gmail_quote">2012/2/9 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><br>
<br>
francesca vitalini wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Tryed the double precision without any success... Again the same type of error message. Might need to try other minimization algorithm. Any suggestions on that?<br>
<br>
</blockquote>
<br></div>
What is the Fmax you achieve, and what are your intents for this process? Minimizing very low is only strictly necessary for certain types of very sensitive calculations. For normal MD, convergence below 100-1000 kJ/mol-nm is typical.<br>
<br>
Other algorithms are listed in the manual. They may or may not be necessary.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2012/2/9 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><div class="h5"><br>
<br>
<br>
<br>
francesca vitalini wrote:<br>
<br>
Hi all!<br>
I'm trying to run some energy minimization with gromacs 3.3.1 on<br>
a system that I have transformed from cg to aa. After the<br>
reverse transformation I solvate the system and I try to<br>
minimize just the proteins (my system is a dimer) keeping fixed<br>
the water. Then the idea would be to minimize the water keeping<br>
the protein in harmonic distance constraints as I just want to<br>
obtain an aa system which describes the configuration obtained<br>
previously in the cg representation.<br>
So, I first use genrestr to create the .itp file for fixing the<br>
position of the water, then I run 10 ps of EM and what I get is<br>
the following error message:<br>
<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 10<br>
<br>
Double precision normally gives you higher accuracy.<br>
You might need to increase your constraint accuracy, or turn<br>
off constraints alltogether (set constraints = none in mdp file)<br>
<br>
From what I've read in previous posts the problem might be<br>
either in the mdp file or in the topology, but I don't<br>
understand what have I made wrong. Here is my mdp file<br>
<br>
<br>
The other possibility is that there is no problem at all. Some<br>
systems cannot be minimized below certain thresholds, based on the<br>
input geometry. You may also want to try a different minimizer or<br>
double precision.<br>
<br></div></div>
<a href="http://www.gromacs.org/__Documentation/Errors#Stepsize___too_small.2c_or_no_change_in___energy._Converged_to_machine___precision.2c_but_not_to_the___requested_precision" target="_blank">http://www.gromacs.org/__<u></u>Documentation/Errors#Stepsize_<u></u>__too_small.2c_or_no_change_<u></u>in___energy._Converged_to_<u></u>machine___precision.2c_but_<u></u>not_to_the___requested_<u></u>precision</a><div>
<div class="h5"><br>
<<a href="http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors#Stepsize_<u></u>too_small.2c_or_no_change_in_<u></u>energy._Converged_to_machine_<u></u>precision.2c_but_not_to_the_<u></u>requested_precision</a>><br>
<br>
-Justin<br>
<br>
Lines starting with ';' ARE COMMENTS<br>
; Everything following ';' is also comment<br>
<br>
title = Energy Minimization ; Title of run<br>
<br>
; The following line tell the program the standard locations<br>
where to find certain files<br>
cpp = /lib/cpp ; Preprocessor<br>
<br>
; Define can be used to control processes<br>
define = -DEPOSRES<br>
;define = -DFLEXIBLE<br>
; Parameters describing what to do, when to stop and what to save<br>
integrator = steep ; Algorithm (steep = steepest<br>
descent minimization)<br>
emtol = 10.0 ; Stop minimization when the<br>
maximum force < 1.0 kJ/mol<br>
dt = 0.005<br>
;nsteps = 2000<br>
nsteps = 5000 ; Maximum number of<br>
(minimization) steps to perform<br>
nstenergy = 1 ; Write energies to disk every<br>
nstenergy steps<br>
energygrps = System ; Which energy group(s) to write<br>
to disk<br>
<br>
; Parameters describing how to find the neighbors of each atom<br>
and how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the<br>
neighbor list<br>
ns_type = grid ; Method to determine neighbor<br>
list (simple, grid)<br>
coulombtype = Reaction-Field ; Treatment of long range<br>
electrostatic interactions<br>
epsilon_rf = 78<br>
rcoulomb = 1.4 ; long range electrostatic cut-off<br>
rvdw = 1.4 ; long range Van der Waals cut-off<br>
constraints = none ; Bond types to replace by<br>
constraints<br>
pbc = xyz ; Periodic Boundary Conditions<br>
(yes/no)<br>
<br>
table-extension = 1.2<br>
<br>
and this is my topology<br>
<br>
;<br>
; File 'dynamin_dimer_fg.top' was generated<br>
; By user: vitalini (213883)<br>
; On host: goat<br>
; At date: Mon Jan 30 11:02:21 2012<br>
;<br>
; This is your topology file<br>
; "The Poodle Chews It" (F. Zappa)<br>
;<br>
; Include forcefield parameters<br>
#include<br></div></div>
"/home/cocktail/vitalini/__<u></u>gromacs_special/share/gromacs/<u></u>__top/ffG53a6m.itp"<div class="im"><br>
<br>
; Include chain topologies<br>
#include "dynamin_dimer_fg_A.itp"<br>
#include "dynamin_dimer_fg_B.itp"<br>
<br>
; Include water topology<br>
#include<br></div>
"/home/cocktail/vitalini/__<u></u>gromacs_special/share/gromacs/<u></u>__top/spc.itp"<div class="im"><br>
<br>
#ifdef POSRES_WATER<br>
; Position restraint for each water oxygen<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>
#endif<br>
<br>
<br>
;Include restraints on water<br>
#ifdef POSRES_WAT<br>
#include "posre_wat.itp"<br>
#endif<br>
<br>
; Include generic topology for ions<br>
#include<br></div>
"/home/cocktail/vitalini/__<u></u>gromacs_special/share/gromacs/<u></u>__top/ions.itp"<div><div class="h5"><br>
<br>
[ system ]<br>
; Name<br>
Protein in water<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein_A 1<br>
Protein_B 1<br>
;SOL 390842<br>
SOL 390820<br>
NA+ 22<br>
<br>
while this is the posre_wat.itp file I generated with genrestr<br>
<br>
; position restraints for non-Protein of Protein in water<br>
<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
15231 1 1000 1000 1000<br>
15232 1 1000 1000 1000<br>
15233 1 1000 1000 1000<br>
15234 1 1000 1000 1000<br>
15235 1 1000 1000 1000<br>
15236 1 1000 1000 1000<br>
15237 1 1000 1000 1000<br>
15238 1 1000 1000 1000<br>
15239 1 1000 1000 1000<br>
15240 1 1000 1000 1000<br>
15241 1 1000 1000 1000<br>
15242 1 1000 1000 1000<br>
15243 1 1000 1000 1000<br>
15244 1 1000 1000 1000<br>
15245 1 1000 1000 1000<br>
15246 1 1000 1000 1000<br>
15247 1 1000 1000 1000<br>
15248 1 1000 1000 1000<br>
15249 1 1000 1000 1000<br>
15250 1 1000 1000 1000<br>
15251 1 1000 1000 1000<br>
..........................<br>
187712 1 1000 1000 1000<br>
<br>
Any help?<br>
Thanks Francesca<br>
<br>
<br>
-- Francesca Vitalini<br>
<br>
PhD student at Computational Molecular Biology Group,<br>
Department of Mathematics and Informatics, FU-Berlin<br>
Arnimallee 6 14195 Berlin<br>
<br>
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<br>
<br>
-- ==============================<u></u>__==========<div class="im"><br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
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<br>
<br>
<br>
<br>
-- <br>
Francesca Vitalini<br>
<br>
PhD student at Computational Molecular Biology Group,<br>
Department of Mathematics and Informatics, FU-Berlin<br>
Arnimallee 6 14195 Berlin<br>
<br>
<a href="mailto:vitalini@zedat.fu-berlin.de" target="_blank">vitalini@zedat.fu-berlin.de</a> <mailto:<a href="mailto:vitalini@zedat.fu-berlin.de" target="_blank">vitalini@zedat.fu-<u></u>berlin.de</a>><br>
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</div></div></blockquote><div class="HOEnZb"><div class="h5">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Francesca Vitalini<br><br>PhD student at Computational Molecular Biology Group, <br>Department of Mathematics and Informatics, FU-Berlin<br>Arnimallee 6 14195 Berlin<br>
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