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><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">
Hi all!<br>
I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation.<br>
So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is 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 either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file<br>
<br>
</blockquote>
<br></div>
The other possibility is that there is no problem at all. Some systems cannot be minimized below certain thresholds, based on the input geometry. You may also want to try a different minimizer or double precision.<br>
<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>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
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 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 descent minimization)<br>
emtol = 10.0 ; Stop minimization when the maximum force < 1.0 kJ/mol<br>
dt = 0.005<br>
;nsteps = 2000<br>
nsteps = 5000 ; Maximum number of (minimization) steps to perform<br>
nstenergy = 1 ; Write energies to disk every nstenergy steps<br>
energygrps = System ; Which energy group(s) to write to disk<br>
<br>
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list<br>
ns_type = grid ; Method to determine neighbor list (simple, grid)<br>
coulombtype = Reaction-Field ; Treatment of long range 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 constraints<br>
pbc = xyz ; Periodic Boundary Conditions (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 "/home/cocktail/vitalini/<u></u>gromacs_special/share/gromacs/<u></u>top/ffG53a6m.itp"<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 "/home/cocktail/vitalini/<u></u>gromacs_special/share/gromacs/<u></u>top/spc.itp"<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 "/home/cocktail/vitalini/<u></u>gromacs_special/share/gromacs/<u></u>top/ions.itp"<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>
-- <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>
</div></div><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>
<a href="mailto:francesca.vitalini@fu-berlin.de" target="_blank">francesca.vitalini@fu-berlin.<u></u>de</a> <mailto:<a href="mailto:francesca.vitalini@fu-berlin.de" target="_blank">francesca.vitalini@fu-<u></u>berlin.de</a>><br>
<br>
<a href="tel:%2B49%203083875776" value="+493083875776" target="_blank">+49 3083875776</a><br>
<a href="tel:%2B49%203083875412" value="+493083875412" target="_blank">+49 3083875412</a><br>
<br>
</blockquote>
<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>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<span class="HOEnZb"><font color="#888888"><br>
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</font></span></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>
<br><a href="mailto:vitalini@zedat.fu-berlin.de" target="_blank">vitalini@zedat.fu-berlin.de</a><br><a href="mailto:francesca.vitalini@fu-berlin.de" target="_blank">francesca.vitalini@fu-berlin.de</a><br><br>+49 3083875776<br>
+49 3083875412<br><br>